Skip to main content Accessibility help
×
×
Home
Computational Phylogenetics
  • Get access
    Check if you have access via personal or institutional login
  • Cited by 3
  • Cited by
    This book has been cited by the following publications. This list is generated based on data provided by CrossRef.

    Nute, Michael Saleh, Ehsan Warnow, Tandy and Faircloth, Brant 2018. Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets. Systematic Biology,

    Roch, Sebastien and Wang, Kun-Chieh 2018. Research in Computational Molecular Biology. Vol. 10812, Issue. , p. 167.

    Molloy, Erin K. and Warnow, Tandy 2018. Comparative Genomics. Vol. 11183, Issue. , p. 260.

    ×

Book description

A comprehensive account of both basic and advanced material in phylogeny estimation, focusing on computational and statistical issues. No background in biology or computer science is assumed, and there is minimal use of mathematical formulas, meaning that students from many disciplines, including biology, computer science, statistics, and applied mathematics, will find the text accessible. The mathematical and statistical foundations of phylogeny estimation are presented rigorously, following which more advanced material is covered. This includes substantial chapters on multi-locus phylogeny estimation, supertree methods, multiple sequence alignment techniques, and designing methods for large-scale phylogeny estimation. The author provides key analytical techniques to prove theoretical properties about methods, as well as addressing performance in practice for methods for estimating trees. Research problems requiring novel computational methods are also presented, so that graduate students and researchers from varying disciplines will be able to enter the broad and exciting field of computational phylogenetics.

Refine List
Actions for selected content:
Select all | Deselect all
  • View selected items
  • Export citations
  • Download PDF (zip)
  • Send to Kindle
  • Send to Dropbox
  • Send to Google Drive
  • Send content to

    To send content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about sending content to .

    To send content items to your Kindle, first ensure no-reply@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle.

    Note you can select to send to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

    Find out more about the Kindle Personal Document Service.

    Please be advised that item(s) you selected are not available.
    You are about to send
    ×

Save Search

You can save your searches here and later view and run them again in "My saved searches".

Please provide a title, maximum of 40 characters.
×
References
Afrasiabi, C., Samad, B., Dineen, D., Meacham, C., and Sjölander, K. 2013. The Phylo-Facts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification. Nucleic Acids Research, 41(W1), W242-W248.
Agarwala, R., and Fernández-Baca, D. 1994. A polynomial-time algorithm for the perfect phylogeny problem when the number of character states is fixed. SIAM Journal on Computing, 23, 1216-1224.
Agarwala, R., and Fernández-Baca, D. 1996. Simple algorithms for perfect phylogeny and triangulating colored graphs. International Journal of Foundations of Computer Science, 7, 11-21.
Agarwala, R., Bafna, V., Farach, M., Paterson, M., and Thorup, M. 1998. On the approximability of numerical taxonomy (fitting distances by tree metrics). SIAM Journal on Computing, 28(3), 1073-1085.
Aho, A., Sagiv, Y., Szymanski, T., and Ullman, J. 1978. Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions. Pages 54-63 of: Proceedings of the 16th Annual Allerton Conference on Communication, Control, and Computing.
Ailon, N., and Charikar, M. 2005. Fitting tree metrics: hierarchical clustering and phylogeny. Pages 73-82 of: 46th Annual IEEE Symposium on Foundations of Computer Science (FOCS–05). doi:10.1109/SFCS.2005.36.
Akaike, H. 1974. A new look at the statistical model identification. IEEE Transactions on Automatic Control, 19, 716-723.
Aldous, D.J. 1991. The continuum random tree II: an overview. Pages 23-70 of: Barlow, M.T., and Bingham, N.H. (eds.), Stochastic Analysis. Cambridge: Cambridge University Press.
Aldous, D.J. 2001. Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today. Statistical Science, 16, 23-34.
Alfaro, M.E., and Holder, M.T. 2006. The posterior and the prior in Bayesian phylogenetics. Annual Review of Ecology, Evolution, and Systematics, 19-42.
Allison, L., Wallace, C.S., and Yee, C.N. 1992a. Finite-state models in the alignment of macromolecules. Journal of Molecular Evolution, 35, 77-89.
Allison, L., Wallace, C.S., and Yee, C.N. 1992b. Minimum message length encoding, evolutionary trees and multiple alignment. Pages 663-674 of: Hawaii International Conference Systems Science, vol. 1.
Allman, E.S., Ané, C., and Rhodes, J. 2008. Identifiability of a Markovian model of molecular evolution with Gamma-distributed rates. Advances in Applied Probability, 40(1), 229-249.
Allman, E.S., Degnan, J.H., and Rhodes, J.A. 2011. Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent. Journal of Mathematical Biology, 62(6), 833-862.
Allman, E., Degnan, J.H., and Rhodes, J. 2016. Species tree inference from gene splits by unrooted STAR methods. IEEE/ACM Transactions on Computional Biology and Bioinformatics. doi: 10.1109/TCBB.2016.2604812.
Altenhoff, A.M., Boeckmann, B., Capella-Gutierrez, S., Dalquen, D.A., et al. 2016. Standardized benchmarking in the quest for orthologs. Nature Methods, 13, 425-430.
Altschul, S.F. 1998. Generalized affine gap costs for protein sequence alignment. Proteins: Structure, Function and Genomics, 32, 88-96.
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403-410.
Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 3389-3402.
Amenta, N., and Klingner, J. 2002. Case study: Visualizing sets of evolutionary trees. Pages 71-74 of: Proceedings of Information Visualization (INFOVIS) 2002.
Amenta, N., Clarke, F., and St. John, K. 2003. A linear-time majority tree algorithm. Pages 216-227 of: Benson, G., and Page, R. (eds.), Proceedings of the Workshop on Algorithms in Bioinformatics (WABI) 2003. Berlin Heidelberg: Springer.
Amir, A., and Keselman, D. 1994. Maximum agreement subtree in a set of evolutionary trees: metrics and efficient algorithms. In: Proceedings of the 35th IEEE Symposium on the Foundations of Computer Science (FOCS).
Ané, C. 2016. PhyloNetworks: analysis for phylogenetic networks in Julia. Software available online at https://github.com/crsl4/PhyloNetworks.jl.
Angiuoli, S.V., and Salzberg, S.L. 2011. Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics, 27(3): 334-342.
Anisimova, M., and Kosiol, C. 2009. Investigating protein-coding sequence evolution with probabilistic codon substitution models. Molecular Biology and Evolution, 26(2), 255-271.
Atteson, K. 1999. The performance of neighbor-joining methods of phylogenetic reconstruction. Algorithmica, 25, 251-278.
Avni, E., Cohen, R., and Snir, S. 2015. Weighted quartets phylogenetics. Systematic Biology, 64(2), 233-242.
Ayling, S.C., and Brown, T.A. 2008. Novel methodology for construction and pruning of quasi-median networks. BMC Bioinformatics, 9, 115.
Bader, D.A., Moret, B.M.E., and Yan, M. 2001. A linear-time algorithm for computing inversion distances between signed permutations with an experimental study. Journal of Computational Biology, 8(5), 483-491.
Bafna, V., and Pevzner, P.A. 1996. Genome rearrangements and sorting by reversals. SIAM Journal on Computing, 25(2), 272-289.
Bafna, V., and Pevzner, P.A. 1998. Sorting by transpositions. SIAM Journal on Discrete Mathematics, 11(2), 224-240.
Bandelt, H.J. 1994. Phylogenetic networks. Verhandl Naturwiss Vereins Hamburg, 34, 51-71.
Bandelt, H.J., and Dress, A.W.M., 1992. Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Molecular Phylogenetics and Evolution, 1, 242-252.
Bandelt, H.J., and Dress, A.W.M., 1993. A relational approach to split decomposition. Pages 123-131 of: Optiz, O., Lausen, B., and Klar, R. (eds.), Information and Classification. Berlin: Springer.
Bandelt, H.J., Macauley, V., and Richards, M. 2000. Median networks: speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA. Molecular Phylogenetics and Evolution, 16, 8-28.
Bansal, M.S., and Eulenstein, O. 2013. Algorithms for genome-scale phylogenetics using gene tree parsimony. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(4), 939-956.
Bansal, M., Burleigh, J.G., Eulenstein, O., and Fernández-Baca, D. 2010. Robinson-Foulds Supertrees. Algorithms for Molecular Biology, 5, 18.
Barthélemy, J.P., and McMorris, F.R. 1986. The median procedure for n-trees. Journal of Classification, 3, 329-334.
Bastkowski, S., Moulton, V., Spillner, A., and Wu, T. 2016. The minimum evolution problem is hard: a link between tree inference and graph clustering problems. Bioinformatics, 32(4), 518-522.
Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Howe, K.L., Marshall, M., and Sonnhammer, E.L.L., 2002. The Pfam protein families database. Nucleic Acids Research, 30, 276-280.
Baum, B.R., and Ragan, M.A. 2004. The MRP method. Pages 17-34 of: Bininda-Emonds, Olaf, R.P. (ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. Dordrecht: Kluwer Academic.
Baum, L.E. 1972. An equality and associated maximization technique in statistical estimation for probabilistic functions of Markov processes. Inequalities, 3, 1-8.
Bayzid, Md. S., and Warnow, T. 2013. Naive binning improves phylogenomic analyses. Bioinformatics, 29(18), 2277-2284.
Bayzid, Md. S., Hunt, T., and Warnow, T. 2014. Disk covering methods improve phylogenomic analyses. BMC Genomics, 15(Suppl 6), S7.
Bayzid, Md. S., Mirarab, S., and Warnow, T. 2013. Inferring optimal species trees under gene duplication and loss. Pages 250-261 of: Pacific Symposium on Biocomputing, vol. 18.
Bayzid, Md. S., Mirarab, S., Boussau, B., and Warnow, T. 2015. Weighted statistical binning: enabling statistically consistent genome-scale phylogenetic analyses. PLoS One, 10(6), 30129183.
Berge, C. 1967. Some classes of perfect graphs. Pages 155-166 of: Harary, F. (ed.), Graph Theory and Theoretical Physics. New York: Academic Press.
Berger, M.P., and Munson, P.J. 1991. A novel randomized iterative strategy for aligning multiple protein sequences. Computer Applications in the Biosciences: CABIOS, 7(4), 479-484.
Berger, S.A., and Stamatakis, A. 2011. Aligning short reads to reference alignments and trees. Bioinformatics, 27(15), 2068-2075.
Berger, S.A., Krompass, D., and Stamatakis, A. 2011. Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood. Systematic Biology, 60(3), 291-302.
Bernardes, J., Zaverucha, G., Vaquero, C., and Carbone, A. 2016. Improvement in protein domain identification is reached by breaking consensus, with the agreement of many profiles and domain co-occurrence. PLoS Computational Biology, 12(7), e1005038.
Berry, A., and Pogorelcnik, R. 2011. A simple algorithm to generate the minimal separators and the maximal cliques of a chordal graph. Information Processing Letters, 111(11), 508-511.
Berry, A., Pogorelcnik, R., and Simonet, G. 2010. An introduction to clique minimal separator decomposition. Algorithms, 3(2), 197-215.
Berry, V., and Bryant, D. 1999. Faster reliable phylogenetic analysis. Page 59-68 of: Proceedings 3rd Annual International Conference on Computational Molecular Biology (RECOMB).
Berry, V., and Gascuel, O. 1997. Inferring evolutionary trees with strong combinatorial evidence. Pages 111-123 of: Proceedings 3rd Annual International Conference on Computing and Combinatorics (COCOON97). Berlin: Springer.
Berry, V., Jiang, T., Kearney, P., Li, M., and Wareham, T. 1999. Quartet cleaning: improved algorithms and simulations. Pages 313-324 of: Proceedings European Symposium on Algorithms (ESA99). Berlin: Springer.
Berry, V., Bryant, D., Kearney, P., Li, M., Jiang, T., Wareham, T., and Zhang, H. 2000. A practical algorithm for recovering the best supported edges in an evolutionary tree. Pages 287-296 of Proceedings ACM/SIAM Symposium on Discrete Algorithms (SODA).
Berthouly, C., Leroy, G., Van, T.N., et al. 2009. Genetic analysis of local Vietnamese chickens provides evidence of gene flow from wild to domestic populations. BMC Genetics, 10(1), 1.
Billera, L.J., Holmes, S.P., and Vogtmann, K. 2001. Geometry of the space of phylogenetic trees. Advances in Applied Mathematics, 27, 733-767.
Binet, M., Gascuel, O., Scornavacca, C., Douzery, E.J.P., and Pardi, F. 2016. Fast and accurate branch lengths estimation for phylogenomic trees. BMC Bioinformatics, 17(1), 23.
Bishop, M.J., and Thompson, E.A. 1986. Maximum likelihood alignment of DNA sequences. Journal of Molecular Biology, 190, 156-165.
Blackburne, B.P., and Whelan, S. 2013. Class of multiple sequence alignment algorithm affect genomic analysis. Molecular Biology and Evolution, 30(3), 642-653.
Blair, J.R.S., and Peyton, B.W. 1993. An introduction to chordal graphs and clique trees. Pages 1-29 of: George, A., et al. (eds.), Graph Theory and Sparse Matrix Computation. New York: Springer.
Blanchette, M., Bourque, G., and Sankoff, D. 1997. Breakpoint phylogenies. Genome Informatics, 8, 25-34.
Blanchette, M., Kunisawa, T., and Sankoff, D. 1999. Gene order breakpoint evidence in animal mitochondrial phylogeny. Journal of Molecular Evolution, 49(2), 193-203.
Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F.A., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., Haussler, D., and Miller, W. 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Research, 14, 708-715.
Bloomquist, E.W., and Suchard, M.A. 2010. Unifying vertical and nonvertical evolution: a stochastic ARG-based framework. Systematic Biology, 59(1), 27-41.
Blum, M.G.B., and Francois, O. 2006. Which random processes describe the Tree of Life? A large-scale study of phylogenetic tree imbalance. Systematic Biology, 55, 685-691.
Bodlaender, H., Fellows, M., and Warnow, T. 1992. Two strikes against perfect phylogeny. Pages 273-283 of: Proceedings 19th International Colloquium on Automata, Languages, and Programming (ICALP). Berlin: Springer.
Bogusz, M., and Whelan, S. 2017. Phylogenetic tree estimation with and without alignment: new distance methods and benchmarking. Systematic Biology, 66(2), 218-231.
Bordewich, M., and Mihaescu, R. 2010. Accuracy guarantees for phylogeny reconstruction algorithms based on balanced minimum evolution. Pages 250-261 of: Moulton, V., and Singh, M. (eds.), Proceedings of the 2010 Workshop on Algorithms for Bioinformatics. Berlin Heidelberg: Springer.
Bordewich, M., and Semple, C. 2016. Determining phylogenetic networks from inter-taxa distances. Journal of Mathematical Biology, 73(2), 283-303. doi:10.1007/s00285-015-0950-8.
Bordewich, M., and Tokac, N. 2016. An algorithm for reconstructing ultrametric tree-child networks from inter-taxa distances. Discrete Applied Mathematics, 213, 47-59.
Bordewich, M., Gascuel, O., Huber, K.T., and Moulton, V. 2009. Consistency of topological moves based on the balanced minimum evolution principle of phylogenetic inference. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 6, 110-117.
Bouchard-Côté, A., and Jordan, M.I. 2013. Evolutionary inference via the Poisson Indel Process. Proceedings of the National Academy of Sciences (USA), 110(4), 1160-1166.
Boussau, B., and Gouy, M. 2006. Efficient likelihood computations with non-reversible models of evolution. Systematic Biology, 5(55), 756-768.
Boussau, B., Szöllʺosi, G.J., Duret, L., Gouy, M., Tannier, E., and Daubin, V. 2013. Genomescale co-estimation of species and gene trees. Genome Research, 23, 323-330.
Bradley, R.K., Roberts, A., Smoot, M., Juvekar, S., Do, J., Dewey, C., Holmes, I., and Pachter, L. 2009. Fast statistical alignment. PLoS Computational Biology, 5(5), e1000392.
Brandstetter, M.G., Danforth, B.N., Pitts, J.P., Faircloth, B.C., Ward, P.S., Buffington, M.L., Gates, M.W., Kula, R.R., and Brady, S.G. 2016. Phylogenomic insights into the evolution of stinging wasps and the origins of ants and bees. Current Biology, 27(7), 1019-1025.
Bray, N., and Pachter, L. 2004. MAVID: constrained ancestral alignment of multiple sequences. Genome Research, 14, 693-699.
Brinkmeyer, M., Griebel, T., and Böcker, S. 2011. Polynomial supertree methods revisited. Advances in Bioinformatics, 2011. Article ID 524182.
Brown, D.G., and Truszkowski, J. 2012. Fast phylogenetic tree reconstruction using locality-sensitive hashing. Pages 14-29 of: International Workshop on Algorithms in Bioinformatics. Berlin Heidelberg: Springer.
Brown, D.P., Krishnamurthy, N., and Sjölander, K. 2007. Automated protein subfamily identification and classification. PLoS Computational Biology, 3(8), 31-60.
Brown, M., Hughey, R., Krogh, A., Mian, I.S., Sjölander, K., and Haussler, D. 1993. Using Dirichlet mixture priors to derive hidden Markov models for protein families. Pages 47-55 of: Proceedings of the First International Conference on Intelligent Systems for Molecular Biology (ISMB).
Brudno, M., Chapman, M., Gottgens, B., Batzoglou, S., and Morgenstern, B. 2003a. Fast and sensitive multiple alignment of long genomic sequences. BMC Bioinformatics, 4:66.
Brudno, M., Do, C., Cooper, G., Kim, M., Davydov, E., NISC Comparative Sequencing Program, Green, E.D., Sidow, A., and Batzoglou, S. 2003b. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Research, 13, 721-731.
Bruno, W.J., Socci, N.D., and Hapern, A.L. 2000. Weighted neighbor joining: a likelihoodbased approach to distance-based phylogeny reconstruction. Molecular Biology and Evolution, 17(1), 189-197.
Bryant, D. 1997. Hunting for trees, building trees and comparing trees: theory and method in phylogenetic analysis. Ph.D. thesis, University of Canterbury, Christchurch, New Zealand.
Bryant, D. 2003. A classification of consensus methods for phylogenetics. Pages 163-184 of: Janowitz, M.F., Lapointe, F.J., McMorris, F.R., Mirkin, B., and Roberts, F.S. (eds.), Bioconsensus. Providence, RI: American Mathematical Society.
Bryant, D. 2005. On the uniqueness of the selection criterion of neighbor-joining. Journal of Classification, 22, 3-15.
Bryant, D., and Moulton, V. 1999. A polynomial time algorithm for constructing the refined Buneman tree. Applied Mathematics Letters, 12, 51-56.
Bryant, D., and Moulton, V. 2002. NeighborNet: an agglomerative method for the construction of planar phylogenetic networks. Pages 375-391 of: Proceeding of Workshop on Algorithms for Bioinformatics. Berlin/Heidelberg: Springer.
Bryant, D., and Steel, M.A. 2001. Constructing optimal trees from quartets. Journal of Algorithms, 38, 237-259.
Bryant, D., and Steel, M.A. 2009. Computing the distribution of a tree metric. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(3), 420-426.
Bryant, D., and Waddell, P. 1998. Rapid evaluation of least-squares and minimum-evolution criteria on phylogenetic trees. Molecular Biology and Evolution, 15, 1346-1359.
Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N.A., and RoyChoudhury, A. 2012. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution, 29(8), 1917-1932.
Bulteau, L., Fertin, G., and Rusu, I. 2011. Sorting by transpositions is difficult. In: Proceedings of the 38th International Colloquium on Automata, Languages, and Programming (ICALP 2011). Berlin: Springer.
Buneman, P. 1971. The recovery of trees from measures of dissimilarity. Pages 387-395 of: Hodson, F., Kendall, D., and Tautu, P. (eds.), Mathematics in the Archaeological and Historical Sciences. Edinburgh: Edinburgh University Press.
Buneman, P. 1974a. A characterization of rigid circuit graphs. Discrete Mathematics, 9(3), 205-212.
Buneman, P. 1974b. A note on the metric properties of trees. Journal of Combinatorial Theory (B), 17, 48-50.
Burleigh, J.G., Eulenstein, O., Fernández-Baca, D., and Sanderson, M.J. 2004. MRF supertrees. Pages 65-86 of: Bininda-Emonds, O.R.P., (ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. Dordrecht: Kluwer Academic.
Burleigh, J.G., Bansal, M.S., Eulenstein, O., Hartmann, S., Wehe, A., and Vision, T.J. 2011. Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees. Systematic Biology, 60(2), 117-125.
Cannone, J.J., Subramanian, S., Schnare, M.N., Collett, J.R., D'Souza, L.M., Du, Y., Feng, B., Lin, N., Madabusi, L.V., Muller, K.M., Pande, N., Shang, Z., Yu, N., and Gutell, R.R. 2002. The Comparative RNA Web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron and other RNAs. BMC Bioinformatics, 3(15).
Capella-Gutiérrez, S., and Galbadón, T. 2013. Measuring guide-tree dependency of inferred gaps for progressive aligners. Bioinformatics, 29(8), 1011-1017.
Cardona, G., Llabrés, M., Rosselló, F., and Valiente, G. 2009. On Nakhleh's metric for reduced phylogenetic networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(4), 629-638.
Cartwright, Reed A. 2006. Logarithmic gap costs decrease alignment accuracy. BMC Bioinformatics, 7(527).
Cavender, J.A. 1978. Taxonomy with confidence. Mathematical Biosciences, 40, 271-280.
Chan, C.X., and Ragan, M.A. 2013. Next-generation phylogenomics. Biology Direct, 8(3).
Chan, C.X., Bernard, G., Poirion, O., Hogan, J.M., and Ragan, M.A. 2014. Inferring phylogenies of evolving sequences without multiple sequence alignment. Scientific Reports, 4: article number 6504.
Chang, J.T. 1996. Full reconstruction of Markov models on evolutionary trees: identifiability and consistency. Mathematical Biosciences, 137, 51-73.
Chang, M., and Benner, S. 2004. Empirical analysis of protein insertions and deletions: determining parameters for the correct placement of gaps in protein sequence alignments. Journal of Molecular Biology, 341, 671-631.
Chaudhary, R. 2015. MulRF: a software package for phylogenetic analysis using multicopy gene trees. Bioinformatics, 31, 432-433.
Chaudhary, R., Bansal, M.S., Wehe, A., Fernández-Baca, D., and Eulenstein, O. 2010. iGTP: a software package for large-scale gene tree parsimony analysis. BMC Bioinformatics, 11, 574.
Chaudhary, R., Burleigh, J.G., and Fernández-Baca, D. 2012. Fast local search for unrooted Robinson-Foulds supertrees. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9, 1004-1013.
Chen, D., Diao, L., Eulenstein, O., Fernández-Baca, D., and Sanderson, M.J. 2003. Flipping: a supertree construction method. Pages 135-160 of: Bioconsensus. Providence, RI: American Mathematical Society.
Chen, D., Eulenstein, O., Fernández-Baca, D., and Burleigh, J.G. 2006. Improved heuristics for minimum-flip supertree construction. Evolutionary Bioinformatics, 2, 401-410.
Chen, M.H., Kuo, L., and Lewis, P.O. (eds.). 2014. Bayesian Phylogenetics: Methods, Algorithms, and Applications. Boca Raton, FL CRC Press.
Chifman, J., and Kubatko, L. 2014. Quartet inference from SNP data under the coalescent. Bioinformatics, 30(23), 3317-3324.
Chifman, J., and Kubatko, L. 2015. Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites. Journal of Theoretical Biology, 374, 35-47.
Chou, J., Gupta, A., Yaduvanshi, S., Davidson, R., Nute, M., Mirarab, S., and Warnow, T. 2015. A comparative study of SVDquartets and other coalescent-based species tree estimation methods. BMC Genomics, 16(Suppl 10), S2.
Collingridge, P., and Kelly, S. 2012. MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments. BMC Bioinformatics, 13: 117.
Cotton, J.A., and Wilkinson, M. 2007. Majority rule supertrees. Systematic Biology, 56(3), 445-452.
Cotton, J.A., and Wilkinson, M. 2009. Supertrees join the mainstream of phylogenetics. Trends in Ecology & Evolution, 24, 1-3.
Criscuolo, A., and Gascuel, O. 2008. Fast NJ-like algorithms to deal with incomplete distance matrices. BMC Bioinformatics, 9(166).
Criscuolo, A., Berry, V., Douzery, E., and Gascuel, O. 2006. SDM: a fast distancebased approach for (super) tree building in phylogenomics. Systematic Biology, 55, 740-755.
Cummings, M.P., Otto, S.P., and Wakeley, J. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Molecular Biology and Evolution, 12, 814-822.
Darling, A.C.E., Mau, B., Blatter, F.R., and Perna, N.T. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Research, 14, 1394-1403.
Darling, A.C.E., Mau, B, and Perna, N.T. 2010. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One, 5(6), e11147.
Darriba, D., Taboada, G.L., Doallo, R., and Posada, D. 2011. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics, 27(8), 1164-1165.
Darriba, D., Taboada, G.L., Doallo, R., and Posada, D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9(8), 772.
Dasarathy, G., Nowak, R., and Roch, S. 2015. Data requirement for phylogenetic inference from multiple loci: a new distance method. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(2), 422-432.
Daskalakis, C., and Roch, S. 2010. Alignment-free phylogenetic reconstruction: sample complexity via a branching process analysis. The Annals of Applied Probability, 23(2), 693-721.
Daskalakis, C., and Roch, S. 2016. Species trees from gene trees despite a high rate of lateral genetic transfer: a tight bound. Pages 1621-1630: Proceedings of the 27th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA).
Daskalakis, C., Mossel, E., and Roch, S. 2006. Optimal phylogenetic reconstruction. Pages 159-168 of: STOC06: Proceedings of the 38th Annual ACM Symposium on Theory of Computing.
Davidson, R., Vachaspati, P., Mirarab, S., and Warnow, T. 2015. Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer. BMC Genomics, 16(Suppl 10), S1.
Day, W.H.E., 1987. Computational complexity of inferring phylogenies from dissimilarity matrices. Bulletin of Mathematical Biology, 49, 461-467.
Day, W.H.E., and Sankoff, D. 1986. Computational complexity of inferring phylogenies by compatibility. Systematic Biology, 35(2), 224-229.
Dayhoff, M.O., Schwartz, R.M., and Orcutt, B.C. 1978. A model of evolutionary change in proteins. Pages 345-352 of: Atlas of Protein Sequence and Structure, vol. 5. Washington, DC: National Biomedical Research Foundation.
De Maio, N., Holmes, I., Schlötterer, C., and Kosiol, C. 2013. Estimating empirical codon hidden Markov models. Molecular Biology and Evolution, 30(3), 725-736.
De Maio, N., Schrempf, D., and Kosiol, C. 2015. PoMo: an allele frequency-based approach for species tree estimation. Systematic Biology, 64(6), 1018-1031.
De Oliveira Martins, L., Mallo, D., and Posada, D. 2016. A Bayesian supertree model for genome-wide species tree reconstruction. Systematic Biology, 65(3), 397-416.
DeBlasio, D., and Kececioglu, J. 2015. Learning parameter-advising sets for multiple sequence alignment. IEEE/ACM Transactions on Computational Biology and Bioinformatics, PP(99), 1.
DeGiorgio, M.I., and Degnan, J.H. 2010. Fast and consistent estimation of species trees using supermatrix rooted triples. Molecular Biology and Evolution, 27(3), 552-569.
DeGiorgio, M., and 2014. Robustness to divergence time underestimation when inferring species trees from estimated gene trees. Systematic Biology, 63(1), 66-82.
Degnan, J.H. 2013. Anomalous unrooted gene trees. Systematic Biology, 62(4), 574-590.
Degnan, J.H., and Rosenberg, N.A. 2006. Discordance of species trees with their most likely gene trees. PLoS Genetics, 2, 762-768.
Degnan, J.H., DeGiorgio, M., Bryant, D., and Rosenberg, N.A. 2009. Properties of consensus methods for inferring species trees from gene trees. Systematic Biology, 58, 35-54.
Della Vedova, G., Jiang, T., Li, J., and Wen, J. 2002. Approximating minimum quartet inconsistency. Pages 894-895 of: Proceedings ACM/SIAM Symposium on Discrete Algorithms (SODA) 2002.
Deng, X., and Cheng, J. 2011. MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts. BMC Bioinformatics, 12, 472.
DeSantis, T.Z., Hugenholtz, P., Keller, K., Brodie, E.L., Larsen, N., Piceno, Y.M., Phan, R., and and erson, G.L. 2006. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Research, 34, W394-399.
Desper, R., and Gascuel, O. 2002. Fast and accurate phylogeny reconstruction algorithm based on the minimum-evolution principle. Journal of Computational Biology, 9, 687-705.
Desper, R., and Gascuel, O. 2004. Theoretical foundations of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted leastsquares tree fitting. Molecular Biology and Evolution, 21(3), 587-598.
Desper, R., and Gascuel, O. 2005. The minimum-evolution distance-based approach to phylogeny inference. Pages 1-32 of: Gascuel, O. (ed.), Mathematics of Evolution and Phylogeny. Oxford: Oxford University Press.
Devroye, L., and Gyʺorfi, L. 1990. No empirical probability measure can converge in the total variation sense for all distributions. The Annals of Statistics, 18(3), 1496-1499.
Dewey, C.N. 2007. Aligning multiple whole genomes with Mercator and MAVID. Methods in Molecular Biology, 395, 221-236.
Dirac, G.A. 1974. On rigid circuit graphs. Abhandlungen aus dem Mathematischen Seminar der Univiversität Hamburg, 25, 71-76.
Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Research, 15(2), 330-340.
Dobzhansky, T. 1973. Nothing in biology makes sense except in the light of evolution. American Biology Teacher, 35, 125-129.
Domelevo-Entfellner, J.B., and Gascuel, O. 2008. Une approche phylo-HMM pour la recherche de séquences. Pages 133-139 of: van Helden, J., and Moreau, Y. (eds.), JOBIM–08: Journées Ouvertes Biologie, Informatique, Mathématiques, vol. 408.
Dotsenko, Y., Coarfa, C., Mellor-Crummey, J., Nakhleh, L., and Roshan, U. 2006. PRec-I-DCM3: a parallel framework for fast and accurate large scale phylogeny reconstruction. International Journal on Bioinformatics Research and Applications (IJBRA), 2, 407-419.
Douady, C.J., Delsuc, F., Boucher, Y., Doolittle, W.F., and Douzery, E.J.P., 2003. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Molecular Biology and Evolution, 20(2), 248-254.
Doyon, J.P., Ranwez, V., Daubin, V., and Berry, V. 2011. Models, algorithms and programs for phylogeny reconciliation. Briefings in Bioinformatics, 12(5), 392-400.
Dress, A., and Steel, M.A. 1992. Convex tree realizations of partitions. Applied Mathematics Letters, 5(3), 3-6.
Du, S.Z., Zhang, Y., and Feng, Q. 1991. On better heuristic for Euclidian Steiner minimum trees. Pages 431-439 of: Proceedings of the 32nd Symposium on the Foundations of Computer Science (FOCS).
Du, Z., Stamatakis, A., Lin, F., Roshan, U., and Nakhleh, L. 2005a. Parallel divideand-conquer phylogeny reconstruction by maximum likelihood. Pages 776-785 of: International Conference on High Performance Computing and Communications. Berlin: Springer.
Du, Z., Lin, F., and Roshan, U. 2005b. Reconstruction of large phylogenetic trees: a parallel approach. Computational Biology and Chemistry, 29(4), 273-280.
Dubchak, I., Poliakov, A., Kislyuk, A., and Brudno, M. 2009. Multiple whole-genome alignments without a reference organism. Genome Research, 19, 682-689.
Durbin, R., Eddy, S., Krogh, A., and Mitchison, G. 1998. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge: Cambridge University Press.
Durrett, R. 2008. Probability Models for DNA Sequence Evolution. Second edition. New York: Springer.
Earl, D., Nguyen, N., Hickey, G., Harris, R.S., Fitzgerald, S., Beal, K., Seledtsov, I., Molodtsov, V., Raney, B.J., Clawson, H., Kim, J., Kemena, C., Chang, J.M., Erb, I., Poliakov, A., Hou, M., Herrero, J., Kent, W. James, Solovyev, V., Darling, A.E., Ma, J., Notredame, C., Brudno, M., Dubchak, I., Haussler, D., and Paten, B. 2014. Alignathon: a competitive assessment of whole-genome alignment methods. Genome Research, 24, 2077-2089.
Eddy, S.R. 2009. A new generation of homology search tools based on probabilistic inference. Genome Informatics, 23, 205-211.
Edgar, R.C. 2004a. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5(113), 113.
Edgar, R.C. 2004b. MUSCLE: a multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792-1797.
Edgar, R.C., and Sjölander, K. 2003. COACH: profile-profile alignment of protein families using hidden Markov models. Bioinformatics, 20(8), 1309-1318.
Edgar, R.C., and Sjölander, K. 2004. A comparison of scoring functions for protein sequence profile alignment. Bioinformatics, 20(8), 1301-1308.
Efron, B., Halloran, E., and Holmes, S. 1996. Bootstrap confidence levels for phylogenetic trees. Proceedings of the National Academy of Science (USA), 93, 13429-13434.
El-Mabrouk, N., and Sankoff, D. 2012. Analysis of gene order evolution beyond singlecopy genes. Pages 397-429 of: Anisimova, M. (ed.), Evolutionary Genomics: Statistical and Computational Methods, vol. 1. Berlin: Springer.
Erdös, P.L., Steel, M.A., Székely, L., and Warnow, T. 1997. Local quartet splits of a binary tree infer all quartet splits via one dyadic inference rule. Computers and Artificial Intelligence, 16(2), 217-227.
Erdös, P.L., Steel, M.A., Székely, L., and Warnow, T. 1999a. A few logs suffice to build (almost) all trees (I). Random Structures and Algorithms, 14, 153-184.
Erdös, P.L., Steel, M.A., Székely, L., and Warnow, T. 1999b. A few logs suffice to build (almost) all trees (II). Theoretical Computer Science, 221, 77-118.
Estabrook, G., Johnson, C., and McMorris, F. 1975. An idealized concept of the true cladistic character. Mathematical Biosciences, 23, 263-272.
Evans, S.N., and Warnow, T. 2005. Unidentifiable divergence times in rates-across-sites models. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1, 130-134.
Ewens, W.J. 2000. Mathematical Population Genetics: I. Theoretical Introduction. Second edition. Berlin: Springer.
Ewens, W.J., and Grant, G.R. 2001. Statistical Methods in Bioinformatics: An Introduction. New York: Springer.
Ezawa, K. 2016. General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable? BMC Bioinformatics, 17(1), 304. erratur, 17, 457.
Faghih, F., and Brown, D.G. 2010. Answer set programming or hypercleaning: where does the magic lie in solving maximum quartet consistency. Technical Report, University of Waterloo, CS-2010-20.
Fakcharoenphol, J., Rao, S., and Talwar, K. 2003. A tight bound on approximating arbitrary metrics by tree metrics. Pages 448-455 of: Proceedings 35th Annual ACM Symposium on the Theory of Computing (STOC). New York ACM Press.
Farach, M., and Thorup, M. 1994. Fast comparison of evolutionary trees. Pages 481-488 of: Proceedings 5th Annual ACM-SIAM Symposium on Discrete Algorithms.
Farris, J.S. 1973. A probability model for inferring evolutionary trees. Systematic Zoology, 22, 250-256.
Felsenstein, J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Systematic Zoology, 27, 401-410.
Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17(6), 368-376.
Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39(4), 783-791.
Felsenstein, J. 2004. Inferring Phylogenies. Sunderland, MA: Sinauer Associates.
Felsenstein, J., and Churchill, G.A. 1996. A hidden Markov model approach to variation among sites in rates of evolution. Molecular Biology and Evolution, 13, 93-104.
Feng, D.F., and Doolittle, R. 1987. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. Journal of Molecular Evolution, 25, 351-360.
Fernández-Baca, D. 2000. The perfect phylogeny problem. Pages 203-234 of: Du, D.Z., and Cheng, X. (eds.), Steiner Trees in Industries. Dordrecht: Kluwer Academic.
Finden, C.R., and Gordon, A.D. 1995. Obtaining common pruned trees. Journal of Classification, 2, 255-276.
Finn, R.D., Clements, J., and Eddy, S.R. 2011. HMMER web server: interactive sequence similarity searching. Nucleic Acids Research, 39, W29-W37.
Fiorini, S., and Joret, G. 2012. Approximating the balanced minimum evolution problem. Operations Research Letters, 40, 31-55.
Fisher, R.A. 1922. On the dominance ratio. Proceedings of the Royal Society of Edinburgh, 42, 321-341.
Fitch, W.M. 1971. Toward defining the course of evolution: minimal change for a specific tree topology. Systematic Zoology, 20, 406-416.
Fitch, W.M., and Margoliash, E. 1967. Construction of phylogenetic trees. Science, 155, 279-284.
Fletcher, W., and Yang, Z. 2009. Indelible: a flexible simulator of biological sequence evolution. Molecular Biology and Evolution, 26(8), 1879-1888.
Fletcher, W., and Yang, Z. 2010. The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Molecular Biology and Evolution, 27(10), 2257-2267.
Foulds, L.R., and Graham, R.L. 1982. The Steiner problem in phylogeny is NP-complete. Advances in Applied Mathematics, 3, 43-49.
Francis, A.R., and Steel, M.A. 2015. Tree-like reticulation networks: when do tree-like distances also support reticulation evolution? Mathematical Biosciences, 259, 12-19.
Frati, F., Simon, C., Sullivan, J., and Swofford, D.L. 1997. Evolution of the mitochondrial COII gene in Collembola. Journal of Molecular Evolution, 44, 145-158.
Frith, M.C., and Kawaguchi, R. 2015. Split-alignment of genomes finds orthologies more accurately. Genome Biology, 16, 106.
Fu, Z., Chen, X., Vacic, V., Nan, P., Zhong, Y., and Jiang, T. 2007. MSOAR: a highthroughput ortholog assignment system based on genome rearrangement. Journal of Computational Biology, 14(9), 1160-1175.
Gaither, J., and Kubatko, L. 2016. Hypothesis tests for phylogenetic quartets, with applications to coalescent-based species tree inference. Journal of Theoretical Biology, 408, 179-186.
Ganapathy, G., and Warnow, T. 2001. Finding the maximum compatible tree for a bounded number of trees with bounded degree is solvable in polynomial time. Pages 156-163 of: Proceedings of the First InternationalWorkshop on Algorithms and Bioinformatics (WABI). Berlin: Springer.
Ganapathy, G., and Warnow, T. 2002. Approximating the complement of the maximum compatible subset of leaves of k trees. Pages 122-134 of: Proceedings of the Fifth International Workshop on Approximation Algorithms for Combinatorial Optimization.
Ganapathy, G., Ramachandran, V., and Warnow, T. 2003. Better hill-climbing seaches for parsimony. Pages 245-258 of: Proceedings of the Third International Workshop on Algorithms in Bioinformatics (WABI).
Ganapathy, G., Ramachandran, V., and Warnow, T. 2004. On contract-and-refinetransformations between phylogenetic trees. Pages 893-902 of: ACM/SIAM Symposium on Discrete Algorithms (SODA–04).
Gardner, D.P., Xu, W., Miranker, D.P., Ozer, S., Cannonne, J., and Gutell, R. 2012. An accurate scalable template-based alignment algorithm. Pages 237-243 of: Proceedings International Conference on Bioinformatics and Biomedicine, 2012.
Gascuel, O. 1997. Concerning the NJ algorithm and its unweighted version, UNJ. Pages 149-170 of: Roberts, F.S., and Rzhetsky, A. (eds.), Mathematical Hierarchies and Biology. Providence, RI American Mathematical Society.
Gascuel, O. 2000. On the optimization principle in phylogenetic analysis and the minimumevolution criterion. Molecular Biology and Evolution, 17(3), 401-405.
Gascuel, O., and Steel, M.A. 2006. Neighbor-joining revealed. Molecular Biology and Evolution, 23(11), 1997-2000.
Gascuel, O., and Steel, M.A. 2016. A “stochastic safety radius” for distance-based tree reconstruction. Algorithmica, 74(4), 1386-1403.
Gascuel, O., Bryant, D., and Denis, F. 2001. Strengths and limitations of the minimum evolution principle. Systematic Biology, 50(5), 621-627.
Gatesy, J.P., and Springer, M.S. 2014. Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Molecular Phylogenetics and Evolution, 80, 231-266.
Gatesy, J., Meredith, R.W., Janecka, J.E., Simmons, M.P., Murphy, W.J., and Springer, M.S. 2016. Resolution of a concatenation/coalescence kertuffle: partitioned coalescence support and a robust family-level tree for Mammalia. Cladistics. DOI: 10.1111/cla.12170.
Gavril, F. 1972. Algorithms for minimum coloring, maximum clique, minimum covering by cliques, and maximum independent set of a chordal graph. SIAM Journal on Computing, 1(2), 180-187.
Gavril, F. 1974. The intersection graphs of subtrees in trees are exactly the chordal graphs. Journal of Combinatorial Theory (B), 16, 47-56.
Ge, F., Wang, L.S., and Kim, J. 2005. The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biology, 3(10), e316.
Gerstein, M.B., Bruce, C., Rozowsky, J.S., Zheng, D., Du, J., Korbel, J.O., Emanuelsson, O., Zhang, Z.D., Weissman, S., and Snyder, M. 2007. What is a gene, post-ENCODE? History and updated definition. Genome Research, 17(6), 669-681.
Giarla, T.C., and Esselstyn, J.A. 2015. The challenges of resolving a rapid, recent radiation: empirical and simulated phylogenomics of Philippine shrews. Systematic Biology, 64(5), 727-740.
Gogarten, J.P., and Townsend, J.P. 2005. Horizontal gene transfer, genome innovation and evolution. Nature Reviews Microbiology, 3(9), 679-687.
Gogarten, J.P., Doolittle, W.F., and Lawrence, J.G. 2002. Prokaryotic evolution in light of gene transfer. Molecular Biology and Evolution, 19(12), 2226-2238.
Goldman, N., and Yang, Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution, 11, 725-736.
Goloboff, P.A. 1999. Analyzing large data sets in reasonable times: solution for composite optima. Cladistics, 15, 415-428.
Golumbic, M. 2004. Algorithmic Graph Theory and Perfect Graphs. Second edition. New York: Elsevier.
Gordon, A.D. 1986. Consensus supertrees: the synthesis of rooted trees containing overlapping sets of labeled leaves. Journal of Classification, 3, 335-348.
Gordon, K., Ford, E., and St. John, K. 2013. Hamiltonian walks of phylogenetic treespaces. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(4), 1076-1079.
Gori, K., Suchan, T., Alvarez, N., Goldman, N., and Dessimoz, C. 2016. Clustering genes of common evolutionary history. Molecular Biology and Evolution, 33(6): 1590-1605.
Gotoh, O. 1990. Consistency of optimal sequence alignments. Bulletin of Mathematical Biology, 52, 509-525.
Gotoh, O. 1994. Further improvement in methods of group-to-group sequence alignment with generalized profile operations. Computer Applications in the Biosciences: CABIOS, 10, 379-387.
Gould, S.J., Raup, D.M., Spekowski, J.J., and Schopf, T.J.M., 1997. The shape of evolution: a comparison of real and random clades. Paleobiology, 3, 23-40.
Grass Phylogeny Working Group. 2001. Phylogeny and subfamilial classification of the grasses (Poacea). Annals of the Missouri Botanical Garden, 88(3), 373-457.
Grauer, D. 2016. Molecular and Genome Evolution. Sunderland, MA: Sinauer Associates.
Grauer, D., and Li, W.H. 2000. Fundamentals of Molecular Evolution. Sunderland, MA: Sinauer Associates.
Graybeal, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Systematic Biology, 47(1), 9-17.
Gribskov, M., McLachlan, A.D., and Eisenberg, D. 1987. Profile analysis: detection of distantly related proteins. Proceedings of the National Academy of Sciences (USA), 84(13), 4355-4358.
Gu, X., and Li, W.H. 1995. The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment. Journal of Molecular Evolution, 40, 464-473.
Guindon, S., and Gascuel, O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52(5), 696-704.
Guo, S.,Wang, L.S., and Kim, J. 2009. Large-scale simulation of RNA macroevolution by an energy-dependent fitness model. arXiv:0912.2326.
Gusfield, D. 1991. Efficient algorithms for inferring evolutionary trees. Networks, 21, 19-28.
Gusfield, D. 1993. Efficient methods for multiple sequence alignment with guaranteed error bounds. Bulletin of Mathematical Biology, 55(1), 141-154.
Gusfield, D. 2014. ReCombinatorics: The Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks. Cambridge, MA: MIT Press.
Guyer, C., and Slowinski, J.B. 1991. Comparisons of observed phylogenetic topologies with null expectations among three monophyletic lineages. Evolution, 45, 340-350.
Hagopian, R., Davidson, J.D., Datta, R.S., Jarvis, G., and Sjölander, K. 2010. SATCHMOJS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction. Nucleic Acids Research, 38 (Web Server Issue), W29-W34.
Hahn, M.W., and Nakhleh, L. 2016. Irrational exuberance for resolved species trees. Evolution, 70(1), 7-17.
Hallett, M.T., and Lagergren, J. 2000. New algorithms for the duplication-loss model. Pages 138-146 of: Proceedings of the Annual International Conference on Research in Compututional Molecular Biology (RECOMB) 2000. New York: ACM Press.
Hallström, B.M., and Janke, A. 2010. Mammalian evolution may not be strictly bifurcating. Molecular Biology and Evolution, 27, 2804-2806.
Hamada, M., and Asai, K. 2012. A classification of bioinformatics algorithms from the viewpoint of Maximizing Expected Accuracy (MEA). Journal of Computational Biology, 19(5), 532-549.
Hannenhalli, S., and Pevzner, P.A. 1995. Transforming men into mice (polynomial algorithm for genomic distance problem). Pages 581-592 of: Proceedings of the 36th Annual Symposium on the Foundations of Computer Science (FOCS).
Hartigan, J.A. 1973. Minimum mutation fits to a given tree. Biometrics, 29(1), 53-65.
Hastings, W.K. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika, 57(1), 97-109.
Haussler, D., Krogh, A.,Mian, I.S., and Sjölander, K. 1993. Protein modelling using hidden Markov models: analysis of globins. Pages 792-802 of: Proceedings Twenty-Sixth Annual Hawaii International Conference on System Sciences, vol. 1. Washington, DC: IEEE Computer Society Press.
Haws, D., Hodge, T.L., and Yoshida, R. 2011. Optimality of the neighbor joining algorithm and faces of the balanced minimum evolution polytope. Bulletin of Mathematical Biology, 73(11).
Heard, S.B., and Mooers, A.O. 2002. Signatures of random and selective mass extinctions in phylogenetic tree balance. Systematic Biology, 51, 889-897.
Heath, T.A., Hedtke, S.M., and Hillis, D.M. 2008. Taxon sampling and the accuracy of phylogenetic analyses. Journal of Systematics and Evolution, 46(3), 239-257.
Hein, J., Jiang, T., Wang, L., and Zhang, K. 1996. On the complexity of comparing evolutionary trees. Discrete Applied Mathematics, 71, 153-169.
Hein, J., Wiuf, C., Knudsen, B., Møller, M.B., and Wibling, G. 2000. Statistical alignment: computational properties, homology testing and goodness-of-fit. Journal of Molecular Biology, 302, 265-279.
Heled, J., and Drummond, A.J. 2010. Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution, 27, 570-580.
Helmkamp, L.J., Jewett, E.M., and Rosenberg, N.A. 2012. Improvements to a class of distance matrix methods for inferring species trees from gene trees. Journal of Computational Biology, 19(6), 632-649.
Hendy, M., and Penny, D. 1989. A framework for the quantitative study of evolutionary trees. Systematic Zoology, 38, 297-309.
Herman, J.L., Challis, C.J., Novák, A., Hein, J., and Schmidler, S.C. 2014. Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure. Molecular Biology and Evolution, 31(9), 2251-2266.
Herman, J.L., Novák, A., Lyngso, R., Szabó, A., Miklós, I., and Hein, J. 2015. Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs. BMC Bioinformatics, 16(1), 1-26.
Higgins, D.G., and Sharp, P.M. 1988. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. GENE, 73(1), 237-244.
Hillis, D.M. 1996. Inferring complex phylogenies. Nature, 383, 130-131.
Hillis, D. 1997. Response from D.M. Hillis. Trends in Ecology & Evolution, 12(9), 358.
Hillis, D.M., Huelsenbeck, J.P., and Swofford, D.L. 1994. Hobgoblin of phylogenetics. Nature, 369, 363-364.
Hillis, D.M., Moritz, C., and Mable, B.K. (eds.). 1996. Molecular Systematics Second edition. Sunderland, MA: Sinauer Associates.
Hillis, D.M., Pollock, D.D., McGuire, J.A., and Zwickl, D.J. 2003. Is sparse taxon sampling a problem for phylogenetic inference? Systematic Biology, 52(1), 124-126.
Hillis, D.M., Heath, T.A., and St. John, K. 2005. Analysis and visualization of tree space. Systematic Biology, 54(3), 471-482.
Hirosawa, M., Totoki, Y., Hoshida, M., and Ishikawa, M. 1995. Comprehensive study on iterative algorithms of multiple sequence alignment. Computer Applications in the Biosciences: CABIOS, 11(1), 13-18.
Hoff, M., Orf, S., Riehm, B., Darriba, D., and Stamatakis, A. 2016. Does the choice of nucleotide substitution models matter topologically? BMC Bioinformatics, 17, 143.
Hogeweg, P., and Hesper, B. 1984. The alignment of sets of sequences and the construction of phyletic trees: an integrated method. Journal of Molecular Evolution, 20, 175-186.
Hohl, M., Kurtz, S., and Ohlebusch, E. 2002. Efficient multiple genome alignment. Bioinformatics, 18, S312-S320.
Holder, M.T., and Lewis, P.O. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nature Reviews Genetics, 43, 275-284.
Holland, B., and Moulton, V. 2003. Consensus networks: a method for visualizing incompatibilities in collections of trees. Pages 165-176 of: Proceedings of the Workshop on Algorithms in Bioinformatics. Berlin: Springer.
Holland, B.R., Huber, K.T., Moulton, V., and Lockhart, P.J. 2004. Using consensus networks to visualize contradictory evidence for species phylogeny. Molecular Biology and Evolution, 21, 1459-1461.
Holland, B.R., Delsuc, F., and Moulton, V. 2005. Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentrals and hexapods. Systematic Biology, 54, 66-76.
Holland, B.R., Jermiin, L.S., and Moulton, V. 2006. Improved consensus network techniques for genome-scale phylogeny. Molecular Biology and Evolution, 23, 848-855.
Holland, B., Conner, G., Huber, K., and Moulton, V. 2007. Imputing supertrees and supernetworks from quartets. Systematic Biology, 56(1), 57-67.
Holmes, I., and Bruno, W.J. 2001. Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics, 17, 803-820.
Holmes, I., and Durbin, R. 1988. Dynamic programming alignment accuracy. Journal of Computational Biology, 5, 493-504.
Holmes, S. 1999. Phylogenies: an overview. Pages 81-118 of: Halloran, M., and Geisser, S. (eds.), Statistics and Genetics New York: Springer-Verlag.
Holmes, S. 2003. Bootstrapping phylogenetic trees: theory and methods. Statistical Science, 18(2), 241-255.
Holmes, S. 2005. Statistical approach to tests involving phylogenies. Pages 91-120 of: Gascuel, O. (ed.), Mathematics of Evolution and Phylogeny. Oxford: Oxford University Press.
Hosner, P.A., Faircloth, B.C., Glenn, T.C., Braun, E.L., and Kimball, R.T. 2016. Avoiding missing data biases in phylogenomic inference: an empirical study in the landfowl (Aves: Galliformes). Molecular Biology and Evolution, 33(4), 1110-1125.
Huang, H., and Knowles, L.L. 2016. Unforeseen consequences of excluding missing data from next-generation sequences: simulation study of RAD sequences. Systematic Biology, 65(3), 357-365.
Huang, H., He, Q., Kubatako, L.S., and Knowles, L.L. 2010. Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods. Systematic Biology, 59, 573-583.
Huang, W., Zhou, G., Marchand, M., Ash, J.R., Morris, D., Dooren, P. Van, Brown, J.M., Gallivan, K.A., and Wilgenbusch, J.C. 2016. TreeScaper: visualizing and extracting phylogenetic signal from sets of trees. Molecular Biology and Evolution, 33(12), 3314-3316.
Hudson, R.R. 1983. Testing the constant-rate neutral allele model with protein sequence data. Evolution, 37, 203-217.
Hudson, R.R. 1991. Gene genealogies and the coalescent process. Pages 1-44 of: Futuyma, D., and Antonovics, J. (eds.), Oxford Surveys in Evolutionary Biology, vol. 7. Oxford: Oxford University Press.
Huelsenbeck, J.P., and Crandall, K.A. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annual Review of Ecology and Systematics, 28, 437-466.
Huelsenbeck, J.P., and Hillis, D.M. 1993. Success of phylogenetic methods in the fourtaxon case. Systematic Biology, 42(3), 247-265.
Huelsenbeck, J.P., Ronquist, F., Nielsen, R., and Bollback, J.P. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science, 294(5550), 2310-2314.
Huson, D.H. 2007. Split networks and reticulate networks. Pages 247-276 of: Gascuel, O., and Steel, M.A. (eds.), Reconstructing Evolution: New Mathematical and Computational Advances. Oxford: Oxford University Press.
Huson, D.H. 2016. SplitsTree4 Software for computing phylogenetic networks. Available online at www.splitstree.org.
Huson, D., Nettles, S., Parida, L.,Warnow, T., and Yooseph, S. 1998. A divide-and-conquer approach to tree reconstruction. In: Proceedings of the Workshop on Algorithms and Experiments (ALEX98). Trento.
Huson, D., Nettles, S., and Warnow, T. 1999a. Disk-covering, a fast converging method for phylogenetic tree reconstruction. Journal of Computational Biology, 6(3), 369-386.
Huson, D., Vawter, L., and Warnow, T. 1999b. Solving large scale phylogenetic problems using DCM2. Pages 118-129 of: Proceedings of the 7th International Conference on Intelligent Systems for Molecular Biology (ISMB–99). Cambridge, MA: AAAI Press.
Huson, D.H., Dezulian, T., Klöpper, T., and Steel, M.A. 2004. Phylognetic super-networks from partial trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1, 151-158.
Huson, D.H., Rupp, R., and Scornavacca, C. 2010. Phylogenetic Networks: Concepts, Algorithms and Applications. Cambridge: Cambridge University Press.
Iantomo, S., Gori, K., Goldman, N., Gil, M., and Dessimoz, C. 2013. Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment. Pages 59-73 of: Russell, D. (ed.), Multiple Sequence Alignment Methods. New York: Springer.
Izquierdo-Carrasco, F., Smith, S., and Stamatakis, A. 2011. Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees. BMC Bioinformatics, 12(1), 470.
Jacox, E., Chauve, C., Szöllʺosi, G.J., Ponty, Y., and Scornavacca, C. 2016. ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony. Bioinformatics, 32(13), 2056-2058.
Janowitz, M.F., Lapointe, F.J., McMorris, F.R., Mirkin, B., and Roberts, F.S. (eds.). 2003. Bioconsensus. Providence, RI: American Mathematical Society.
Jansen, R., and Palmer, J. 1987. A chloroplast DNA inversion marks an ancient evolutionary split in the sunflower family (Asteraceae). Proceedings of the National Academy of Sciences (USA), 84, 5818-5822.
Jarvis, E., Mirarab, S., Aberer, A., et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215), 1320-1331.
Jewett, E.M., and Rosenberg, N.A. 2012. iGLASS: an improvement to the GLASS method for estimating species trees from gene trees. Journal of Computational Biology, 19(3), 293-315.
Jiang, T., Kearney, P., and Li, M. 2001. A polynomial time approximation scheme for inferring evolutionary trees from quartet topologies and its application. SIAM Journal on Computing, 30, 1942-1961.
Jin, G., Nakhleh, L., Snir, S., and Tuller, T. 2006. Maximum likelihood of phylogenetic networks. Bioinformatics, 22, 2604-2611.
Jin, G., Nakhleh, L., Snir, S., and Tuller, T. 2007. Inferring phylogenetic networks by the maximum parsimony criterion: a case study. Molecular Biology and Evolution, 24(1), 324-337.
Joly, S., McLenachan, P.A., and Lockhart, P.J. 2009. A statistical approach for distinguishing hybridization and incomplete lineage sorting. The American Naturalist, 174(2), E54-E70.
Jones, D.T., Taylor, W.R., and Thornton, J.M. 1992. The rapid generation of mutation data matrices from protein sequences. Computing Applications in the Biosciences (CABIOS), 8, 275282. doi:10.1093/bioinformatics/8.3.275.
Jones, G., Sagitov, S., and Oxelman, B. 2013. Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting. Systematic Biology, 62(3), 476-478.
Jones, S., and Thornton, J.M. 1996. Principles of protein-protein interactions. Proceedings of the National Academy of Sciences (USA), 93(1), 13-20.
Jukes, T.H., and Cantor, C.R. 1997. Evolution of protein molecules. Pages 21-132 in Munro, H.N. (ed.), Mammalian Protein Metabolism. New York: Academic Press.
Kannan, S., and Warnow, T. 1997. A fast algorithm for the computation and enumeration of perfect phylogenies when the number of character states is fixed. SIAM Journal on Computing, 26(6), 1749-1763.
Kannan, S., Warnow, T., and Yooseph, S. 1995. Computing the local consensus of trees. SIAM Journal on Computing, 27(6), 1695-1724.
Kaplan, H., Shamir, R., and Tarjan, R.E. 1997. Faster and simpler algorithm for sorting signed permutations by reversals. Pages 344-351 of: Proceedings of the ACM/SIAM Symposium on Discrete Algorithms (SODA).
Karp, R.M. 1972. Reducibility among combinatorial problems. Pages 85-103 of: Complexity of Computer Computations. New York: Plenum.
Karpinski, M., and Zelikovsky, A. 1997. New approximation algorithms for the Steiner Tree problems. Journal of Combinatorial Optimization, 1(1), 47-65.
Katoh, K., and Toh, H. 2007. PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. Bioinformatics, 23(3), 372-374.
Katoh, K., Kuma, K., Miyata, T., and Toh, H. 2005. Improvement in the acccuracy of multiple sequence alignment MAFFT. Genome Informatics, 16, 22-33.
Kececioglu, J.D. 1993. The maximum weight trace problem in multiple sequence alignment. Pages 106-119 of: Annual Symposium on Combinatorial Pattern Matching. Berlin: Springer.
Kececioglu, J., and Sankoff, D. 1995. Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement. Algorithmica, 13(1-2), 180-210.
Kececioglu, J., and Starrett, D. 2004. Aligning alignments exactly. Pages 85-96 of: Proceedings 8th ACM Conference on Research in Computational Molecular Biology (RECOMB).
Kececioglu, J., and Zhang, W. 1998. Aligning alignments. Pages 189-208 of: Combinatorial Pattern Matching Berlin: Springer.
Kececioglu, J., Kim, E., and Wheeler, T. 2010. Aligning protein sequences with predicted secondary structure. Journal of Computational Biology, 17(3), 561-580.
Kemena, C., and Notredame, C. 2009. Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics, 25, 2455-2465.
Kendall, D.G. 1948. On the generalized “birth-death” process. Annual Review Mathematical Statistics, 19, 1-15.
Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. 2003. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proceedings National Academy of Sciences (USA), 100, 11484-11489.
Kidd, K.K., and Sgaramella-Zonta, L.A. 1971. Phylogenetic analysis: concepts and methods. American Journal of Human Genetics, 23, 235-252.
Kim, J. 1996. General inconsistency conditions for maximum parsimony: effects of branch lengths and increasing numbers of taxa. Systematic Biology, 45, 363-374.
Kim, J., and Ma, J. 2014. PSAR-Align: improving multiple sequence alignment through probabilistic sampling. Bioinformatics, 30(7), 1010-1012.
Kim, J., and Salisbury, B.A. 2001. A tree obscured by vines: horizontal gene transfer and the median tree method of estimating species phylogeny. Pages 571-582 of: Proceedings of the Pacific Symposium of Computing, vol. 6.
Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111-120.
Kingman, J.F.C., 1982. The coalescent. Stochastic Processes and Applications, 13, 235-248.
Knowles, L.L., and Kubatko, L.S. (eds.). 2011. Estimating Species Trees: Practical and Theoretical Aspects. Hoboken, NJ: John Wiley and Sons.
Koch, M.A., Dobes, C., Kiefer, C., Schmickl, R., Klimes, L., and Lysak, M.A. 2007. Supernetwork identifies multiple events of plastid trnF(GAA) pseudogene evolution in the Brassicaceae. Molecular Biology and Evolution, 24(1), 63-73.
Kolaczkowski, B., and Thornton, J.W. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature, 431, 980-984.
Kosiol, C., Bofkin, L., and Whelan, S. 2006. Phylogenetics by likelihood: evolutionary modeling as a tool for understanding the genome. Journal Biomedical Informatics, 39, 51-61.
Kosiol, C., Holmes, I., and Goldman, N. 2007. An empirical codon model for protein sequence evolution. Molecular Biology and Evolution, 24(7), 1464-1479.
Kozlov, A.M., Aberer, A.J., and Stamatakis, A. 2015. ExaML version 3: a tool for phylogenomic analyses on supercomputers. Bioinformatics, 31(15), 2577.
Kreidl, M. 2011. Note on expected internode distances for gene trees in species trees. arXiv:1108.5154v1.
Krishnamurthy, N., Brown, D., and Sjölander, K. 2007. FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function. BMC Evolutionary Biology, 7(1), 1-11.
Krogh, A., Brown, M., Mian, I., Sjölander, K., and Haussler, D. 1994. Hidden Markov models in computational biology: applications to protein modeling. Journal of Molecular Biology, 235, 1501-1531.
Kruskal, J.B. 1956. On the shortest spanning subtree of a graph and the travelling salesman problem. Proceedings of the American Mathematical Society, 7, 48-50.
Kubatko, L.S. 2009. Identifying hybridization events in the presence of coalescence via model selection. Systematic Biology, 58(5), 478-488.
Kubatko, L., and Chifman, J. 2015. An invariants-based method for efficient identification of hybrid species from large-scale genomic data. bioRxiv: 034348.
Kubatko, L.S., and Degnan, J.H. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biology, 56, 17.
Kubatko, L.S., Carstens, B.C., and Knowles, L.L. 2009. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics, 25(7), 971-973.
Kuhner, M.K., and Felsenstein, J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution, 11(3), 459-468.
Kullback, S. 1987. Letter to the editor: The Kullback-Leibler distance. The American Statistician, 41(4), 340-341.
Kupczok, A. 2011. Split-based computation of majority rule supertrees. BMC Evolutionary Biology, 11.
Lacey, M.R., and Chang, J.T. 2006. A signal-to-noise analysis of phylogeny estimation by neighbor-joining: insufficiency of polynomial length sequences. Mathematical Biosciences, 199(2), 188-215.
Lafond, M., and Scornavacca, C. 2016. On theWeighted Quartet Consensus problem. arXiv preprint arXiv:1610.00505.
Lagergren, J. 2002. Combining polynomial running time and fast convergence for the Disk- Covering Method. Journal of Computer and System Science, 65(3), 481-493.
Lanfear, R., Calcott, B., Ho, S.Y.W., and Guindon, S. 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution, 29(6), 1695-1701.
Lapointe, F.J., and Cucumel, G. 1997. The average consensus procedure: combination of weighted trees containing identical or overlapping sets of taxa. Systematic Biology, 46(2), 306-312.
Lapointe, F.J., Wilkinson, M., and Bryant, D. 2003. Matrix representations with parsimony or with distances: two sides of the same coin? Systematic Biology, 52, 865-868.
Larget, B., Kotha, S.K., Dewey, C.N., and Ané, C. 2010. BUCKy: Gene tree/species tree reconciliation with the Bayesian concordance analysis. Bioinformatics, 26(22), 2910-2911.
Leaché, A.D., Chavez, A.S., Jones, L.N., Grummer, J.A., Gottscho, A.D., and Linkem, C.W. 2015. Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing. Genome Biology and Evolution, 7(3), 706-719.
Leavitt, S.D., Grewe, F., Widhelm, T., Muggia, L., Wray, B., and Lumbsch, H.T. 2016. Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches. Scientific Reports, 6(22262). doi: 10.1038/srep22262.
Lechner, M., Hernandez-Rosales, M., Doerr, D., Wieseke, N., Thévenin, A., Stoye, J., Hartmann, R.K., Prohaska, S.J., and Stadler, P.F. 2014. Orthology detection combining clustering and synteny for very large datasets. PLoS ONE, 9(8), e105015. doi:10.1371/journal.pone.0105015.
Lecointre, G.H., Philippe, H., Van Le, H.L., and Le Guyader, H. 1994. How many nucleotides are required to resolve a phylogenetic problem? The use of a new statistical method applicable to available sequences. Molecular Phylogenetics and Evolution, 3, 292-309.
Leebens-Mack, J., Raubeson, L.A., Cui, L., Kuehl, J.V., Fourcade, M.H., Chumley, T.W., Boore, J.L., Jansen, R.K., and dePamphilis, C.W. 2005. Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone. Molecular Biology and Evolution, 22(10), 1948-1963.
Lefort, V., Desper, R., and Gascuel, O. 2015. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Molecular Biology and Evolution, 32(10), 2798-2800.
Leimer, H.G. 1993. Optimal decomposition by clique separators. Discrete Mathematics, 113, 99-123.
Lemmon, E.M., and Lemmon, A.R. 2013. High-throughput genomic data in systematics and phylogenetics. Annual Review of Ecology, Evolution, and Systematics, 44, 99-121.
LeQuesne, W.J. 1969. A method of selection of characters in numerical taxonomy. Systematic Zoology, 18, 201-205.
Li, C., Medlar, A., and Löytynoja, A. 2016. Co-estimation of phylogeny-aware alignment and phylogenetic tree. bioRxiv, 077503. doi: https://doi.org/10.1101.07750.
Li, W.H. 1997. Molecular Evolution. Sunderland, MA: Sinauer Associates, Inc.
Li, W.H., and Tanimura, M. 1987. The molecular clock runs more slowly in man than in apes and monkeys. Nature, 326(6108), 93-96.
Lin, Y., and Moret, B. 2008. Estimating true evolutionary distances under the DCJ model. Bioinformatics, 24(13), i114-i122.
Lin, Y., Rajan, V., and Moret, B. 2012a. A metric for phylogenetic trees based on matching. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(4), 1014-1022.
Lin, Y., Rajan, V., and Moret, B. 2012b. TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis. Bioinformatics, 28(24), 3324-3325.
Liu, K., and Warnow, T. 2012. Treelength optimization for phylogeny estimation. PLoS One, 7(3), e33104.
Liu, K., Raghavan, S., Nelesen, S., Linder, C.R., and Warnow, T. 2009a. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science, 324(5934), 1561-1564.
Liu, K., Linder, C.R., and Warnow, T. 2012a. RAxML and FastTree: comparing two methods for large-scalemaximum likelihood phylogeny estimation. PLoS ONE, 6(11), e27731.
Liu, K.,Warnow, T., Holder,M.T., Nelesen, S.M., Yu, J., Stamatakis, A.P., and Linder, C.R. 2012b. SATé-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Systematic Biology, 61(1), 90-106.
Liu, L., and Yu, L. 2011. Estimating species trees from unrooted gene trees. Systematic Biology, 60(5), 661-667.
Liu, L., Yu, L., Pearl, D.K., and Edwards, S.V. 2009b. Estimating species phylogenies using coalescence times among sequences. Systematic Biology, 58(5), 468-477.
Liu, L., Yu, L., and Edwards, S.V. 2010. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evolutionary Biology, 10(1), 302.
Lockhart, P., Novis, P., Milligan, B.G., Riden, J., Rambaut, A., and Larkum, T. 2006. Heterotachy and tree building: a case study with Plastids and Eubacteria. Molecular Biology and Evolution, 23(1), 40-45.
Lopez, P., Casane, D., and Philippe, H. 2002. Heterotachy, an important process of protein evolution. Molecular Biology and Evolution, 19(1), 1-7.
Löytynoja, A., and Goldman, N. 2005. An algorithm for progressive multiple alignment of sequences with insertions. Proceedings of the National Academy of Sciences (USA), 102, 10557-10562.
Löytynoja, A., and Goldman, N. 2008a. A model of evolution and structure for sequence alignment. Philosophical Transactions of the Royal Society (B), 363, 3913-3919.
Löytynoja, A., and Goldman, N. 2008b. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science, 320(5883), 1632-1635.
Löytynoja, A., Vilella, A.J., and Goldman, N. 2012. Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics, 28, 1685-1691.
Lunter, G.A., Miklós, I., Drummond, A., Jensen, J.L., and Hein, J. 2003a. Bayesian phylogenetic inference under a statistical indel model. Lecture Notes in Bioinformatics, Proceedings of the Workshop on Algorithms for Bioinformatics (WABI) 2003, 2812, 228-244.
Lunter, G.A., Miklos, I., Song, Y.S., and Hein, J. 2003b. An efficient algorithm for statistical multiple alignment on arbitrary phylogenetic trees. Journal of Computational Biology, 10, 869-889.
Lunter, G.A., Miklós, I., Drummond, A., Jensen, J.L., and Hein, J. 2005a. Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics, 6, 83.
Lunter, G.A., Drummond, A.J., Miklós, I., and Hein, J. 2005b. Statistical alignment: recent progress, new applications, and challenges. Pages 375-406 of: Nielsen, R. (ed.), Statistical Methods in Molecular Evolution (Statistics for Biology and Health). Berlin: Springer.
Ma, B.,Wang, Z., and Zhang, K. 2003. Alignment between two multiple alignments. Pages 254-265 of: Proceedings of the 14th Annual Conference on Combinatorial Pattern Matching. Berlin, Heidelberg: Springer.
Ma, J., Zhang, L., Suh, B.B., Raney, B.J., Burhans, R.C., Kent, W.J., Blanchette, M., Haussler, D., and Miller, W. 2006. Reconstructing contiguous regions of an ancestral genome. Genome Research, 16(12), 1557-1565.
Ma, J., Wang, S., Wang, Z., and Xu, J. 2014. MRFalign: protein homology detection through alignment of Markov random fields. PLoS Computational Biology, 10(3), e1003500. doi:10.1371/journal.pcbi.1003500.
Maddison, D. 1991. The discovery and importance of multiple islands of most parsimonious trees. Systematic Zoology, 40, 315-328.
Maddison, D. 2016. The rapidly changing landscape of insect phylogenetics. Current Opinion in Insect Science, 18, 77-82.
Maddison, W.P. 1997. Gene trees in species trees. Systematic Biology, 46, 523-536.
Mallet, J. 2005. Hybridization as an invasion of the genome. Trends in Ecology & Evolution, 20, 229-237.
Mallo, D., and Posada, D. 2016. Multilocus inference of species trees and DNA barcoding. Philosophical Transactions of the Royal Society (B), 371, 20150335. http://dx.doi.org/10.1098/rstb.2015.0335.
Matsen, F.A., Kodner, R.B., and Armbrust, E.V. 2010. pplacer: linear time maximumlikelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics, 11, 538.
McCormack, J., Harvey, M., Faircloth, B., Crawford, N., Glenn, T., and Brumfield, R. 2013. A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS One, 8, 54848.
McKenzie, A., and Steel, M.A. 2001. Properties of phylogenetic trees generated by Yuletype speciation models. Mathematical Biosciences, 170, 91-112.
McMorris, F.R., Warnow, T.J., and Wimer, T. 1994. Triangulating vertex-colored graphs. SIAM Journal on Discrete Mathematics, 7(2), 296-306.
Meiklejohn, K.A., Faircloth, B.C., Glenn, T.C., Kimball, R.T., and Braun, E.L. 2016. Analysis of a rapid evolutionary radiation using ultraconserved elements: evidence for a bias in some multispecies coalescent methods. Systematic Biology, 65(4), 612-627.
Meng, C., and Kubatko, L.S. 2009. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model. Theoretical Population Biology, 75, 35-45.
Metzler, D. 2003. Statistical alignment based on fragment insertion and deletion models. Bioinformatics, 19(4), 490-499.
Mihaescu, R., and Pachter, L. 2008. Combinatorics of least-squares trees. Proceedings of the National Academy of Sciences (USA), 105(36), 13206-13211.
Mihaescu, R., Levy, D., and Pachter, L. 2009. Why neighbor-joining works. Algorithmica, 54(1), 1-24.
Miklós, I. 2003. Algorithm for statistical alignment of sequences derived from a Poisson sequence length distribution. Discrete Applied Mathematics, 127(1), 79-84.
Miklós, I., Lunter, G.A., and Holmes, I. 2004. A “long indel model” for evolutionary sequence alignment. Molecular Biology and Evolution, 21(3), 529-540.
Miller, W., and Myers, E. 1988. Sequence comparison with concave weighting functions. Bulletin of Mathematical Biology, 50, 97-120.
Mindell, D.P. 2013. The Tree of Life: metaphor, model, and heuristic device. Systematic Biology 62(3), 478-489.
Mir arabbaygi (Mirarab), S. 2015. Novel scalable approaches for multiple sequence alignment and phylogenomic reconstruction. Ph.D. thesis, University of Texas at Austin.
Mirarab, S., and Warnow, T. 2011. FastSP: linear-time calculation of alignment accuracy. Bioinformatics, 27(23), 3250-3258.
Mirarab, S., and Warnow, T. 2015. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics, 31(12), i44-i52.
Mirarab, S., Nguyen, N., and Warnow, T. 2012. SEPP: SATé-enabled phylogenetic placement. Pages 247-58 of: Pacific Symposium on Biocomputing.
Mirarab, S., Reaz, R., Bayzid, Md. S., Zimmermann, T., Swenson, M.S., and Warnow, T. 2014a. ASTRAL: Accurate Species TRee ALgorithm. Bioinformatics, 30(17), i541-i548.
Mirarab, S., Bayzid, Md. S., Boussau, B., and Warnow, T. 2014b. Statistical binning improves phylogenomic analysis. Science, 346(6215), 1250463.
Mirarab, S., Nguyen, N., Wang, L.S., Guo, S., Kim, J., and Warnow, T. 2015a. PASTA: ultra-large multiple sequence alignment of nucleotide and amino acid sequences. Journal of Computational Biology, 22, 377-386.
Mirarab, S., Bayzid, M.S., Boussau, B., and Warnow, T. 2015b. Response to comment on “Statistical binning enables an accurate coalescent-based estimation of the avian tree.” Science, 350(6257), 171.
Mitchison, G.J. 1999. A probabilistic treatment of phylogeny and sequence alignment. Journal of Molecular Evolution, 49, 11-22.
Mitchison, G.J., and Durbin, R.M. 1995. Tree-based maximum likelihood substitution matrices and hidden Markov models. Journal of Molecular Evolution, 41, 1139-1151.
Money, D., and Whelan, S. 2012. Characterizing the phylogenetic tree-search problem. Systematic Biology, 61(2), 228-239.
Mooers, A.O. 2004. Effects of tree shape on the accuracy of maximum likelihood-based ancestor reconstructions. Systematic Biology, 53(5), 809-814.
Mooers, A., and Heard, S.B. 1997. Inferring evolutionary process from phylogenetic tree shape. Quantitative Review of Biology, 72(1), 31-54.
Moret, B.M.E., Roshan, U., and Warnow, T. 2002. Sequence length requirements for phylogenetic methods. Pages 343-356 of: Proceedings of the 2nd International Workshop on Algorithms in Bioinformatics (WABI–02). Berlin: Springer.
Moret, B.M.E., Lin, Y., and Tang, J. 2013. Rearrangements in phylogenetic inference: compare, model, or encode? Pages 147-171 of: Chauve, C., El-Mabrouk, N., and Tannier, E. (eds.), Models and Algorithms for Genome Evolution. London: Springer.
Morgenstern, B., Dress, A., and Wener, T. 1996. Multiple DNA and protein sequence based on segment-to-segment comparison. Proceedings of the National Academy of Sciences (USA), 93, 12098-12103.
Morgenstern, B., Frech, K., Dress, A., and Werner, T. 1998. DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics, 14(3), 290-294.
Morlon, H., Potts, M.D., and Plotkin, J.B. 2010. Inferring the dynamics of diversification: a coalescent approach. PLoS Biology, 8(9), e1000493.
Morrison, D.A. 2006. Multiple sequence alignment for phylogenetic purposes. Australian Systematic Botany, 19, 479-539.
Morrison, D. 2010a. Phylogenetic networks in systematic biology (and elsewhere). Pages 1-48 of: Mohan, R. (ed.), Research Advances in Systematic Biology. Trivandrum: Global Research Network.
Morrison, D.A. 2010b. Using data-display networks for exploratory data analysis in phylogenetic studies. Molecular Biology and Evolution, 27(5), 1044-1057.
Morrison, D.A. 2011. Introduction to Phylogenetic Networks. Uppsala: RJR Productions.
Morrison, D.A. 2014a. Is the Tree of Life the best mataphor, model, or heuristic for phylogenetics? Systematic Biology, 63(4), 628-638.
Morrison, D.A. 2014b. Next generation sequencing and phylogenetic networks. EMBnet. journal, 20, 3760.
Morrison, D.A. 2017. Next Generation Systematics. - Peter D. Olson, Joseph Hughe and James A. Cotton. Systematic Biology, 66(1), 121-123. doi: https://doi.org/10.1093/sysbio/syw081.
Morrison, D.A., Morgan, M.J., and Kelchner, S.A. 2015. Molecular homology and multiple-sequence alignment: an analysis of concepts and practice. Australian Systematic Biology, 28, 46-62.
Mossel, E., and Roch, S. 2011. Incomplete lineage sorting: consistent phylogeny estimation from multiple loci. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(1), 166-171.
Mossel, E., and Roch, S. 2013. Identifiability and inference of non-parametric ratesacross-sites models on large-scale phylogenies. Journal of Mathematical Biology, 67, 767-797.
Mossel, E., and Roch, S. 2015. Distance-based species tree estimation: informationtheoretic trade-off between number of loci and sequence length under the coalescent. arXiv preprint. arXiv:1504.05289v1. To appear, The Annals of Applied Probability.
Moyle, R.G., Oliveros, C.H., and ersen, M.J., Hosner, P.A., Benz, B.W., Manthey, J.D., Travers, S.L., Brown, R.M., and Faircloth, B.C. 2016. Tectonic collision and uplift of Wallacea triggered the global songbird radiation. Nature Communications, 7.
Nadeau, J.H., and Taylor, B.A. 1984. Lengths of chromosome segments conserved since divergence of man and mouse. Proceedings of the National Academy of Sciences (USA), 81, 814-818.
Nakhleh, L. 2010. A metric on the space of reduced phylogenetic networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(2), 218-222.
Nakhleh, L. 2016. Computational approaches to species phylogeny inference and gene tree reconciliation. Trends in Ecology ' Evolution, 28, 719-728.
Nakhleh, L., Roshan, U., St. John, K., Sun, J., and Warnow, T. 2001a. Designing fast converging phylogenetic methods. Bioinformatics, 17, 190-198.
Nakhleh, L., Roshan, U., St. John, K., Sun, J., and Warnow, T. 2001b. The performance of phylogenetic methods on trees of bounded diameter. Pages 189-203 of: Proceedings 1st Workshop on Algorithms in BioInformatics (WABI01). Berlin: Springer.
Nakhleh, L., Moret, B.M.E., Roshan, U., St. John, K., Sun, J., and Warnow, T. 2002. The accuracy of fast phylogenetic methods for large datasets. Pages 211-222 of: Proceedings of the 7th Pacific Symposium on Biocomputing (PSB02).
Nakhleh, L., Sun, J., Warnow, T., Linder, C.R., Moret, B.M.E., and Tholse, A. 2003. Towards the development of computational tools for evaluating phylogenetic network reconstruction methods. Pages 315-326 of: Proceedings of the 8th Pacific Symposium on Biocomputing (PSB 2003).
Nakhleh, L., Warnow, T., and Linder, C.R. 2004. Reconstructing reticulate evolution in species: theory and practice. Pages 337-346 of: Proceedings of the 8th International Conference on Computational Molecular Biology (RECOMB–04). New York: ACM Press.
Nakhleh, L., Warnow, T., Linder, C.R., and St. John, K. 2005a. Reconstructing reticulate evolution in species: theory and practice. Journal of Computational Biology, 12(6), 796-811.
Nakhleh, L., Ruths, D., and Wang, L.S. 2005b. RIATA-HGT: A fast and accurate heuristic for reconstructing horizontal gene transfer. Pages 84-93 of: The Eleventh International Computing and Combinatorics Conference (COCOON–05). Berlin: Springer.
Nawrocki, E.P. 2009. Structural RNA homology search and alignment using covariance models. Ph.D. thesis, Washington University in Saint Louis, School of Medicine.
Nawrocki, E.P., Kolbe, D.L., and Eddy, S.R. 2009. Infernal 1.0: inference of RNA alignments. Bioinformatics, 25, 1335-1337.
Needleman, S.B., and Wunsch, C.D. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48, 443-453.
Nei, M. 1986. Stochastic errors in DNA evolution and molecular phylogeny. Pages 515-534 of: Karlin, S., and Nevo, E. (eds.), Evolutionary Processes and Theory. New York: Academic Press.
Nei, M., Kumar, S., and Kumar, S. 2003. Molecular Evolution and Phylogenetics. Oxford: Oxford University Press.
Nelesen, S. 2009. Improved methods for phylogenetics. Ph.D. thesis, University of Texas at Austin.
Nelesen, S., Liu, K., Zhao, D., Linder, C.R., and Warnow, T. 2008. The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses. Pages 15-24 of: Pacific Symposium on Biocomputing, vol. 13.
Nelesen, S., Liu, K., Wang, L.S., Linder, C.R., and Warnow, T. 2012. DACTAL: divideand- conquer trees (almost) without alignments. Bioinformatics, 28, i274-i282.
Neuwald, A.F. 2009. Rapid detection, classification, and accurate alignment of up to a million or more related protein sequences. Bioinformatics, 25, 1869-1875.
Neves, D.T., and Sobral, J.L. 2017. Parallel SuperFine: a tool for fast and accurate supertree estimation - features and limitations. Future Generation Computer Systems, 67, 441-454.
Neves, D.T., Warnow, T., Sobral, J.L., and Pingali, K. 2012. Parallelizing SuperFine. Pages 1361-1367 of: 27th Symposium on Applied Computing (ACM-SAC), Bioinformatics. ACM. doi: 10.1145/2231936.2231992.
Neyman, J. 1971. Molecular studies of evolution: a source of novel statistical problems. Page 127 of: Gupta, S.S., and Yackel, J. (eds.), Statistical Decision Theory and Related Topics. New York: Academic Press.
Nguyen, L.T., Schmidt, H.A., von Haeseler, A., and Minh, B.Q. 2015a. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32(1), 268-274.
Nguyen, N., Mirarab, S., and Warnow, T. 2012. MRL and SuperFine+MRL: new supertree methods. Algorithms for Molecular Biology, 7(3).
Nguyen, N., Mirarab, S., Liu, B., Pop, M., and Warnow, T. 2014. TIPP: taxonomic identification and phylogenetic profiling. Bioinformatics, 30(24), 3548-3555.
Nguyen, N., Mirarab, S., Kumar, K., and Warnow, T. 2015b. Ultra-large alignments using phylogeny aware profiles. Genome Biology, 16(124).
Nguyen, N., Nute, M., Mirarab, S., and Warnow, T. 2016. HIPPI: highly accurate protein family classification with ensembles of hidden Markov models. BMC Bioinformatics, 17 (Suppl 10), 765.
Nixon, K.C. 1999. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics, 15, 407-414.
Notredame, C., Holm, L., and Higgins, D.G. 1998. COFFEE: an objective function for multiple sequence alignments. Bioinformatics, 14(5), 407-422.
Notredame, C., Higgins, D.G., and Heringa, J. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology, 302, 205-217.
Noutahi, E., Semeria, M., Lafond, M., Seguin, J., Boussau, B., Guégen, L., and El-Mabrouk, N. 2015. Efficient gene tree correction guided by species and synteny evolution. HAL archive, https://hal.archives-ouvertes.fr/hal-01162963v2.
Novák, Á., Miklós, I., Lyngsoe, R., and Hein, J. 2008. Stat Align: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. Bioinformatics, 24, 2403-2404.
Nute, M., and Warnow, T. 2016. Scaling statistical multiple sequence alignment to large datasets. BMC Bioinformatics, 17(Suppl 10), 764.
Nye, T.M.W., 2008. Tree of trees: an approach to comparing multiple alternative phylogenies. Systematic Biology, 57, 785-794.
Ogden, T.H., and Rosenberg, M.S. 2006. Multiple sequence alignment accuracy and phylogenetic inference. Systematic Biology, 55(2), 314-328.
Ogden, T.H., and Rosenberg, M. 2007. Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP*. Systematic Biology, 56(2), 182-193.
Ohno, S. 1970. Evolution by Gene Duplication. New York: Springer.
Oldman, J., Wu, T., and van Iersel, L. 2016. TriLoNet: piecing together small networks to reconstruct reticulate evolutionary histories. Molecular Biology and Evolution, 33(8), 2151-2162.
Olson, P.D., Hughes, J., and Cotton, J.A. (eds.). 2016. Next Generation Systematics. Cambridge: Cambridge University Press.
Ortuno, F.M., Valenzuela, O., Pomares, H., Rojas, F., Florido, J.P., Urquiza, J.M., and Rojas, I. 2013. Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques. Nucleic Acids Research, 41(1).
O'Sullivan, O., Suhre, K., Abergel, C., Higgins, D.G., and Notredame, C. 2004. 3DCoffee: combining protein sequences and structure within multiple sequence alignments. Journal of Molecular Biology, 340, 385-395.
Page, R. 2002. Modified Mincut Supertrees. Pages 537-551 of: Guigó, R., and Gusfield, D. (eds.), Algorithms in Bioinformatics. Berlin: Springer.
Page, R., and Holmes, E. 1998. Molecular Evolution: A Phylogenetic Approach. Oxford: Blackwell Publishers.
Pais, F.S.-M., Ruy, P.d.C., Oliveira, G., and Coimbra, R.S. 2014. Assessing the efficiency of multiple sequence alignment programs. Algorithms for Molecular Biology, 9, 4.
Pamilo, P., and Nei, M. 1998. Relationship between gene trees and species trees. Molecular Biology and Evolution, 5, 568-583.
Papadopoulos, J.S., and Agarwala, R. 2007. COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics, 23(9), 1073-1079.
Pardi, F., Guillemot, S., and Gascuel, O. 2012. Combinatorics of distance-based tree inference. Proceedings of the National Academy of Sciences (USA), 109(41), 16443-16448.
Patel, S., Kimball, R.T., and Braun, E.L. 2013. Error in phylogenetic estimation for bushes in the Tree of Life. Journal of Phylogenetics and Evolutionary Biology, 1, 110. doi:10.4172/2329-9002.1000110.
Paten, B., Herrero, J., Beal, K., Fitzgerald, S., and Birney, E. 2008. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Research, 18, 1814-1828.
Paten, B., Herrero, J., Beal, K., and Birney, E. 2009. Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinformatics, 25(3), 295-301.
Paten, B., Earl, D., Nguyen, N., Diekhans, M., Zerbino, D., and Haussler, D. 2011. Cactus: algorithms for genome multiple sequence alignment. Genome Research, 21, 1512-1528.
Pauplin, Y. 2000. Direct calculation of a tree length using a distance matrix. Molecular Biology and Evolution, 51, 41-47.
Pe'er, I., and Shamir, R. 1998. The median problems for breakpoints are NP-complete. In: Electronic Colloquium on Computational Complexity, vol. 71.
Pei, J., and Grishin, N.V. 2006. MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Research, 34, 4364-4374.
Pei, J., and Grishin, N.V. 2007. PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics, 23, 802-808.
Pei, J., Sadreyev, R., and Grishin, N.V. 2003. PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics, 19, 427-428.
Penn, O., Privman, E., Landan, G., Graur, D., and Pupko, T. 2010. An alignment confidence score capturing robustness to guide tree uncertainty. Molecular Biology and Evolution, 27(8), 1759-1767.
Pennisi, E. 2016. Shaking up the Tree of Life. Science, 354, 817-821.
Phillimore, A.B., and Price, T.D. 2008. Density-dependent cladogenesis in birds. PLoS Biology, 6(3), e71.
Phillips, C.A., and Warnow, T. 1996. The asymmetric median tree: a new model for building consensus trees. Discrete Applied Mathematics, 71, 311-335.
Phuong, T.M., Do, C.B., Edgar, R.C., and Batzoglou, S. 2006. Multiple alignment of protein sequences with repeats and rearrangements. Nucleic Acids Research, 34(20), 5932-5942.
Poe, S. 2003. Evaluation of the strategy of long-branch subdivision to improve the accuracy of phylogenetic methods. Systematic Biology, 52, 423-428.
Pollock, D.D., Zwickl, D.J., McGuire, J.A., and Hillis, D.M. 2002. Increased taxon sampling is advantageous for phylogenetic inference. Systematic Biology, 51, 664-671.
Posada, D. 2016. Phylogenomics for systematic biology. Systematic Biology, 65, 353-356.
Posada, D., and Buckley, T.R. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Systematic Biology, 53(5), 793-808.
Posada, D., and Crandall, K.A. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics, 14(9), 817-818.
Posada, D., and Crandall, K.A. 2001. Selecting the best-fit model of nucleotide substitution. Systematic Biology, 50(4), 580-601.
Pray, L.A. 2004. Epigenetics: genome, meet your environment - as the evidence for epigenetics, researchers reacquire a taste for Lamarckism. The Scientist, 14.
Preusse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W., Peplies, J., and Glockner, F.O. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research, 35, 718-796.
Price, M.N., Dehal, P.S., and Arkin, A.P. 2010. FastTree 2: approximately maximumlikelihood trees for large alignments. PLoS ONE, 5(3), e9490. doi:10.1371/journal. pone.0009490.
Purvis, A., and Quicke, D.L.J., 1997a. Are big trees indeed easy? Reply from A. Purvis and D.L.J. Quicke. Trends in Ecology & Evolution, 12(9), 357-358.
Purvis, A., and Quicke, D.L.J., 1997b. Building phylogenies: are the big easy? Trends in Ecology & Evolution, 12(2), 49-50.
Qian, B., and Goldstein, R.A. 2001. Distribution of indel lengths. Proteins, 45, 102-104.
Qian, B., and Goldstein, R.A. 2003. Detecting distant homologs using phylogenetic treebased HMMs. PROTEINS: Structure, Function, and Genetics, 52, 446-453.
Rannala, B., and Yang, Z. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. Journal of Molecular Evolution, 43, 304-311.
Rannala, B., and Yang, Z. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics, 164, 1645-1656.
Rannala, B., Huelsenbeck, J.P., Yang, Z., and Nielsen, R. 1998. Taxon sampling and the accuracy of large phylogenies. Systematic Biology, 47, 702-710.
Ranwez, V., and Gascuel, O. 2001. Quartet-based phylogenetic inference: improvements and limits. Molecular Biology and Evolution, 18(6), 1103-1116.
Ranwez, V., Criscuolo, A., and Douzery, E.J. 2010. SuperTriplets: a triplet-based supertree approach to phylogenomics. Bioinformatics, 26(12), i115-i123.
Raphael, B., Zhi, D., Tang, H., and Pevzner, P. 2004. A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Research, 14, 2336-2346.
Rasmussen, M.D., and Kellis, M. 2012. Unified modelling of gene duplication, loss, and coalescence using a locus tree. Genome Research, 22, 755-765.
Raubeson, L.A., and Jansen, R.K. 1992. Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science, 255, 1697-1699.
Raup, D.M. 1985. Mathematical models of cladogenesis. Paleobiology, 11(1), 42-52.
Raup, D.M., Gould, S.J., Schopf, T.J.M., and Simberloff, D.S. 1973. Stochastic-models of phylogeny and the evolution of diversity. Journal of Geology, 81, 525-542.
Reaz, R., Bayzid, M.S., and Rahman, M.S. 2014. Accurate phylogenetic tree reconstruction from quartets: a heuristic approach. PLoS One. doi: 10.1371/journal.pone.0104008.
Redelings, B.D., and Suchard, M.A. 2005. Joint Bayesian estimation of alignment and phylogeny. Systematic Biology, 54(3), 401-418.
Reeck, G.R., de Haen, C., Teller, D.C., Doolitte, R., Fitch, W., Dickerson, R.E., Chambon, P., McLachlan, A.D., Margoliash, E., Jukes, T.H., and Zuckerkandl, E. 1987. “Homology” in proteins and nucleic acids: a terminology muddle and a way out of it. Cell, 50, 667.
Rheindt, F.E., Fujita, M.K., Wilton, P.R., and Edwards, S.V. 2014. Introgression and phenotypic assimilation in Zimmerius flycatchers (Tyrannidae): population genetic and phylogenetic inferences from genome-wide SNPs. Systematic Biology, 63(2), 134-152.
Rieseberg, L.H. 1997. Hybrid origins of plant species. Annual Review of Ecology and Systematics, 28, 359-389.
Rivas, E., and Eddy, S.R. 2008. Probabilistic phylogenetic inference with insertions and deletions. PLoS Computational Biology, 4(9), e1000172.
Rivas, E., and Eddy, S.R. 2015. Parameterizing sequence alignment with an explicit evolutionary model. BMC Bioinformatics, 16(1).
Roch, S. 2006. A short proof that phylogenetic tree reconstruction by maximum likelihood is hard. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(1), 92-94.
Roch, S. 2008. Sequence-length requirement for distance-based phylogeny reconstruction: breaking the polynomial barrier. Pages 729-738 of: Proceedings of the Symposium on Foundations of Computer Science (FOCS).
Roch, S. 2010. Towards extracting all phylogenetic information from matrices of evolutionary distances. Science, 327(5971), 1376-1379.
Roch, S., and Sly, A. 2016. Phase transition in the sample complexity of likelihood-based phylogeny inference. arXiv:1508.01964.
Roch, S., and Snir, S. 2013. Recovering the tree-like trend of evolution despite extensive lateral genetic transfer: a probabilistic analysis. Journal of Computational Biology, 20, 93-112.
Roch, S., and Steel, M.A. 2015. Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent. Theoretical Population Biology, 100, 56-62.
Roch, S., and Warnow, T. 2015. On the robustness to gene tree estimation error (or lack thereof) of coalescent-based species tree methods. Systematic Biology, 64(4), 663-676.
Ronquist, F., and Huelsenbeck, J.P. 2003. Mr Bayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
Ronquist, F., Huelsenbeck, J.P., and Britton, T. 2004. Bayesian supertrees. Pages 193-224 of: Bininda-Emonds, O.R.P., (ed.), Phylogenetic Supertrees. New York: Springer.
Rose, D.J. 1970. Triangulated graphs and the elimination process. Journal of Mathematical Analysis and Applications, 32, 597-609.
Rose, D.J., Tarjan, R.E., and Lueker, G.S. 1976. Algorithmic aspects of vertex elimination on graphs. SIAM Journal on Computing, 5(2), 266-283.
Rosenberg, N.A. 2002. The probability of topological concordance of gene trees and species trees. Theoretical Population Biology, 61(2), 225-247.
Rosenberg, N.A. 2013. Discordance of species trees with their most likely gene trees: a unifying principle. Molecular Biology and Evolution, 30(12), 2709-2013.
Roshan, U., and Livesay, D.R. 2006. Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics, 22, 2715-2721.
Roshan, U., Moret, B.M.E., Warnow, T., and Williams, T.L. 2004. Rec-I-DCM3: a fast algorithmic technique for reconstructing large phylogenetic trees. In: Proceedings of the IEEE Computational Systems Bioinformatics Conference (CSB).
Rusinko, J., and McParlon, M. 2017. Species tree estimation using neighbor joining. Journal of Theoretical Biology, 414, 5-7.
Rzhetsky, A., and Nei, M. 1993. Theoretical foundation of the minimum evolution method of phylogenetic inference. Molecular Biology and Evolution, 10(5), 1073-1095.
Sadreyev, R., and Grishin, N. 2003. COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. Journal of Molecular Biology, 326, 317-336.
Saitou, N., and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406-425.
Sanderson, M.J., and Shaffer, H.B. 2002. Troubleshooting molecular phylogenetic analyses. Annual Review of Ecology and Systematics, 33(1), 49-72.
Sankoff, D. 1975. Minimal mutation trees of sequences. SIAM Journal of Applied Mathematics, 28(1), 35-42.
Sankoff, D., and Blanchette, M. 1998. Multiple genome rearrangement and breakpoint phylogeny. Journal of Computational Biology, 5(3), 555-570.
Sankoff, D., and Cedergren, R.J. 1983. Simultaneous comparison of three or more sequences related by a tree. Pages 253-264 of: Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison. Boston, MA.
Sankoff, D., and Rousseau, P. 1975. Locating the vertices of a Steiner tree in an arbitrary metric space. Mathematical Programming, 9, 240-246.
Sankoff, D., Leduc, G., Antoine, N., Paquin, B., Lang, B.F., and Cedergren, R. 1992. Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. Proceedings of the National Academy of Sciences (USA), 89(14), 6575-6579.
Sankoff, D., Abel, Y., and Hein, J. 1994. A tree- a window- a hill; generalization of nearestneighbor interchange in phylogenetic optimization. Journal of Classification, 11(2), 209-232.
Sattath, S., and Tversky, A. 1977. Additive similarity trees. Psychometrika, 42(3), 319-345.
Schrempf, D., Minh, B.Q., De Maio, N., von Haeseler, A., and Kosiol, C. 2016. Reversible polymorphism-aware phylogenetic models and their application to tree inference. Journal of Theoretical Biology, 407, 362-370.
Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D., and Miller, W. 2003. Human-mouse alignments with BLASTZ. Genome Research, 13(1), 103-107.
Schwarz, G. 1978. Estimating the dimension of a model. Annals of Statistics, 6, 461-464.
Schwikowski, B., and Vingron, M. 1997. The deferred path heuristic for the generalized tree alignment problem. Journal of Computational Biology, 4(3), 415-431.
Schwikowski, B., and Vingron, M. 2003. Weighted sequence graphs: boosting iterated dynamic programming using locally suboptimal solutions. Discrete Applied Mathematics, 127(1), 95-117.
Semple, C., and Steel, M.A. 2000. A supertree method for rooted trees. Discrete Applied Mathematics, 105(13), 147-158.
Sevillya, G., Frenkel, Z., and Snir, S. 2016. Triplet MaxCut: a new toolkit for rooted supertree. Methods in Ecology and Evolution, 7(11), 1359-1365.
Shao, M., and Moret, B.M.E., 2016. On computing breakpoint distances for genomes with duplicate genes. Pages 189-203 of: Singh, M. (ed.), Proceedings of the 28th Annual Conference for Research in Computational Molecular Biology (RECOMB 2016). New York: Springer.
Shigezumi, T. 2006. Robustness of greedy type minimum evolution algorithms. Pages 815-821 of: Proceedings of the International Conference on Computational Science. Berlin: Springer.
Siepel, A., and Haussler, D. 2004. Combining phylogenetic and hidden Markov models in biosequence analysis. Journal of Computational Biology, 11(2-3), 413-428.
Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W., Lopez, R.,McWilliams, H., Remmert, M., Soding, J., Thompson, J.D., and Higgins, D. 2011. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7.
Sievers, F., Dineen, D., Wilm, A., and Higgins, D.G. 2013. Making automated multiple alignments of very large numbers of protein sequences. Bioinformatics, 29(8), 989-995.
Sjölander, K. 2004. Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics, 20(2), 170-179.
Sjölander, K., Karplus, K., Brown, M.P., Hughey, R., Krogh, A., Mian, I.S., and Haussler, D. 1996. Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Computing Applications in the Biosciences (CABIOS), 12, 327-45.
Sjölander, K., Datta, R.S., Shen, Y., and Shoffner, G.M. 2011. Ortholog identification in the presence of domain architecture rearrangement. Briefings in Bioinformatics, 12(5), 413-422.
Smith, J.V., Braun, E.L., and Kimball, R.T. 2013. Ratite non-monophyly: independent evidence from 40 novel loci. Systematic Biology, 62(1), 35-49.
Smith, S.A., Beaulieu, J.M., and Donoghue, M.J. 2009. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evolutionary Biology, 9, 37.
Smith, T.F., and Waterman, M.S. 1981. Identification of common molecular subsequences. Journal of Molecular Biology, 147, 195-197.
Snir, S., and Rao, S. 2006. Using Max Cut to enhance rooted trees consistency. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(4), 323-333.
Snir, S., and Rao, S. 2010. Quartets MaxCut: a divide and conquer quartets algorithm. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(4), 704-718.
Snir, S., Warnow, T., and Rao, S. 2008. Short quartet puzzling: a new quartet-based phylogeny reconstruction algorithm. Journal of Computational Biology, 15(1), 91-103.
Söding, J. 2005. Protein homology detection by HMM-HMM comparison. Bioinformatics, 21(7), 951-960.
Sokal, R., and Michener, C. 1958. A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin, 38, 1409-1438.
Solís-Lemus, C., and Ané, C. 2016. Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting. PLoS Genetics, 12(3), e1005896.
Spencer, M., Bordalejo, B., Wang, L.S., Barbrook, A.C., Mooney, L.R., Robinson, P., Warnow, T., and Howe, C.J. 2003. Gene order analysis reveals the history of The Canterbury Tales manuscripts. Computers and the Humanities, 37(1), 97-109.
Springer, M.S., and Gatesy, J. 2016. The gene tree delusion. Molecular Phylogenetics and Evolution, 94, 1-33.
St. John, K. 2016. Review paper: the shape of phylogenetic treespace. Systematic Biology. doi:10.1093/sysbio/syw025.
St. John, K., Warnow, T., Moret, B.M.E., and Vawter, L. 2003. Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining. Journal of Algorithms, 48, 173-193.
Stadler, T., and Degnan, J.H. 2012. A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree. Algorithms for Molecular Biology, 7(7).
Stamatakis, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688-2690.
Steel, M.A. 1992. The complexity of reconstructing trees from qualitative characters and subtrees. Journal of Classification, 9, 91-116.
Steel, M.A. 1994a. The maximum likelihood point for a phylogenetic tree is not unique. Systematic Biology, 43(4), 560-564.
Steel, M.A. 1994b. Recovering a tree from the leaf colourations it generates under a Markov model. Applied Mathematics Letters, 7, 19-24.
Steel, M.A. 2013. Consistency of Bayesian inference of resolved phylogenetic trees. Journal of Theoretical Biology, 336, 246-249.
Steel, M.A., and Gascuel, O. 2006. Neighbor-joining revealed. Molecular Biology and Evolution, 23(11), 1997-2000.
Steel, M.A., and Rodrigo, A. 2008. Maximum likelihood supertrees. Systematic Biology, 57(2), 243-250.
Steel, M.A., and Warnow, T. 1993. Kaikoura tree theorems: the maximum agreement subtree problem. Information Processing Letters, 48, 77-82.
Steel, M.A., Linz, S., Huson, D.H., and Sanderson, M.J. 2013. Identifying a species tree subject to random lateral gene transfer. Journal of Theoretical Biology, 322, 81-93.
Stockham, C., Wang, L.S., and Warnow, T. 2002. Postprocessing of phylogenetic analysis using clustering. Bioinformatics 18(Supp.1), i285-i293.
Stolzer, M., Lai, H., Xu, M., Sathaye, D., Vernot, B., and Durand, D. 2012. Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. Bioinformatics, 28(18), i409-i415.
Stoye, J., Evers, D., and Meyer, F. 1998. Rose: generating sequence families. Bioinformatics, 14(2), 157-163.
Strimmer, K., and Moulton, V. 2000. Likelihood analysis of phylogenetic networks using directed graphical models. Molecular Biology and Evolution, 17(6), 875-881.
Strimmer, K, and von Haeseler, A. 1996. Quartet puzzling: a quartet maximim-likelihood method for reconstructing tree topologies. Molecular Biology and Evolution, 13(7), 964-969.
Studier, J.A., and Keppler, K.L. 1988. A note on the neighbor-joining algorithm of Saitou and Nei. Molecular Biology and Evolution, 5(6), 729-731.
Sturtevant, A., and Dobzhansky, T. 1936. Inversions in the third chromosome of wild races of Drosophila pseudoobscura and their use in the study of the history of the species. Proceedings of the National Academy of Sciences (USA), 22, 448-450.
Subramanian, A.R., Kaufmann, M., and Morgenstern, B. 2008. DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. Algorithms for Molecular Biology, 3, 6.
Suchard, M.A., and Redelings, B.D. 2006. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics, 22, 2047-2048.
Sugiura, N. 1978. Further analysis of the data by Akaike's information criterion and the finite corrections. Communications in Statistics: Theory and Methods, 7(1), 13-26.
Sullivan, J., and Joyce, P. 2005. Model selection in phylogenetics. Annual Review of Ecology, Evolution, and Systematics, 36, 445-466.
Sullivan, J., and Swofford, D.L. 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. Journal of Mammalian Evolution, 4, 77-86.
Sun, K., Meiklejohn, K.A., Faircloth, B.C., Glenn, T.C., Braun, E.L., and Kimball, R.T. 2014. The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach. Proceedings of the Royal Society of London (B): Biological Sciences, 281(1790), 20140823.
Swenson, K.M., Doroftei, A., and El-Mabrouk, N. 2012a. Gene tree correction for reconciliation and species tree inference. Algorithms for Molecular Biology, 7(1), 1-11.
Swenson, M.S., Barbançon, F., Linder, C.R., and Warnow, T. 2010. A simulation study comparing supertree and combined analysis methods using SMIDGen. Algorithms for Molecular Biology, 5, 8.
Swenson, M.S., Suri, R., Linder, C.R., and Warnow, T. 2011. An experimental study of Quartets MaxCut and other supertree methods. Algorithms for Molecular Biology, 6, 7.
Swenson, M.S., Suri, R., Linder, C.R., and Warnow, T. 2012b. SuperFine: fast and accurate supertree estimation. Systematic Biology, 61(2), 214-227.
Swofford, D.L. 2002. PAUP*: Phylogenetic Analysis Using Parsimony (* And Other Methods) Ver. 4. Sunderland, MA: Sinauer Associates.
Swofford, D.L., Olson, G.J., Waddell, P.J., and Hillis, D.M. 1996. Phylogenetic Inference. Second edition. Sunderland, MA: Sinauer Associates.
Syvanen, M. 1985. Cross-species gene transfer; implications for a new theory of evolution. Journal of Theoretical Biology, 112, 333-343.
Szöllʺosi, G.J., Boussau, B., Abby, S.S., Tannier, E., and Daubin, V. 2012. Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proceedings of the National Academy of Sciences (USA), 109, 17513-17518.
Szöllʺosi, G.J., Rosikiewicz, W., Boussau, B., Tannier, E., and Daubin, V. 2013. Efficient exploration of the space of reconciled gene trees. Systematic Biology, 62(6), 901-912.
Szöllʺosi, G.J., Tannier, E., Daubin, V., and Boussau, B. 2015. The inference of gene trees with species trees. Systematic Biology, 64, E42-E62.
Takahashi, H., and Matsuyama, A. 1980. An approximate solution for the Steiner problem in graphs. Mathematica Japonica, 24, 463-470.
Talavera, G., and Castresana, J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology, 56, 564-577.
Taly, J.F., Magis, C., Bussotti, G., Chang, J.M., Tommaso, P.D., Erb, I., Espinosa-Carrasco, J., Kemena, C., and Notredame, C. 2011. Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures. Nature Protocols, 6, 1669-1682.
Tan, G., Muffato, M., Ledergerber, C., Herrero, J., Goldman, N., Gil, M., and Dessimoz, C. 2015. Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference. Systematic Biology, 64(5), 778-791.
Tang, J., and Moret, B.M.E., 2003. Scaling up accurate phylogenetic reconstruction from gene-order data. Bioinformatics, 19 (Suppl. 1), i305-i312.
Tarjan, R.E. 1985. Decomposition by clique separators. Discrete Mathematics, 55, 221-232.
Tavaré, S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Pages 57-86 of: Lectures on Mathematics in the Life Sciences, vol. 17. Providence, RI: American Mathematical Society.
Taylor, M.S., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y., and Semple, C.A.M., 2006. Heterotachy in mammalian promoter evolution. PLoS Genetics, 2(4), e30.
Than, C., and Nakhleh, L., 2009. Species tree inference by minimizing deep coalescences. PLoS Computational Biology, 5, 31000501.
Thompson, J., Plewniak, F., and Poch, O. 1999. BAliBASE: a benchmark alignments database for the evaluation of multiple sequence alignment programs. Bioinformatics, 15, 87-88. Extended collection of benchmarks is available at www-bio3d-igbmc.ustrasb.fr/balibase/.
Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting,position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673-4680.
Thorley, J.L., and Wilkinson, M. 2003. A view of supertree methods. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 61, 185-194.
Thorne, J.L., Kishino, H., and Felsenstein, J. 1991. An evolutionary model for maximum likelihood alignment of DNA sequences. Journal of Molecular Evolution, 33(2), 114-124.
Thorne, J.L., Kishino, H., and Felsenstein, J. 1992. Inching toward reality: an improved likelihood model of sequence evolution. Journal of Molecular Evolution, 34(1), 3-16.
Toth, A., Hausknecht, A., Krisai-Greilhuber, I., Papp, T., Vagvolgyi, C., and Nagy, L.G. 2013. Iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family Bolbitiaceae. PLoS One, 8(2), e56143.
Tuffley, C., and Steel, M.A. 1997. Links between maximum likelihood and maximum parsimony under a simple model of site substitution. Bulletin of Mathematical Biology, 59, 581-607.
Tukey, J.W. 1997. Exploratory Data Analysis. Reading, MA: Addison-Wesley.
Ullah, I., Parviainen, P., and Lagergren, J. 2015. Species tree inference using a mixture model. Molecular Biology and Evolution, 32(9), 2469-2482.
Uricchio, L.H., Warnow, T., and Rosenberg, N.A. 2016. An analytical upper bound on the number of loci required for all splits of a species tree to appear in a set of gene trees. BMC Bioinformatics, 17(14), 241.
Vach, W. 1989. Least squares approximation of additive trees. Pages 230-238 of: Opitz, O. (ed.), Conceptual and Numerical Analysis of Data. Berlin: Springer.
Vachaspati, P., and Warnow, T. 2015. ASTRID: Accurate Species TRees from Internode Distances. BMC Genomics, 16(Suppl 10), S3.
Vachaspati, P., and Warnow, T. 2016. FastRFS: fast and accurate Robinson- Foulds Supertrees using constrained exact optimization. Bioinformatics. doi: 10.1093/bioinformatics/btw600.
Varón, A.,