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Encyclopedia > Phylogenetics software

This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees. Such tools are commonly used in comparative genomics, cladistics, and bioinformatics. Computational phylogenetics is the study of computational algorithms, methods and computer programs for use in phylogenetic analyses. ... It has been suggested that Evolutionary tree be merged into this article or section. ... // Overview Comparative genomics is the study of relationships between the genomes of different species. ... This cladogram shows the relationship among various insect groups. ... Map of the human X chromosome (from the NCBI website). ...

NAME Description Methods Link Author
PHYLIP Phylogenetic inference package Maximum parsimony, distance matrix, maximum likelihood download J. Felsenstein
PAUP Phylogenetic analysis using parsimony Maximum parsimony, distance matrix, maximum likelihood purchase D. Swofford
PAML Phylogenetic analysis by maximum likelihood Maximum likelihood download Z. Yang
ClustalW Progressive multiple sequence alignment Distance matrix/nearest neighbor EBI PBIL EMBNet GenomeNet Thompson et al.
QuickTree Tree construction optimized for efficiency Neighbor-joining server K. Howe, A. Bateman, R. Durbin
MOLPHY Molecular phylogenetics (protein or nucleotide) Maximum likelihood server J. Adachi and M. Hasegawa
TreeGen Tree construction given precomputed distance data Distance matrix server ETH Zurich
fastDNAml Optimized maximum likelihood (nucleotides only) Maximum likelihood download G.J. Olsen
TREE-PUZZLE Maximum likelihood and statistical analysis Maximum likelihood download H.A. Schmidt, K. Strimmer, A. von Haeseler
TreeAlign Efficient hybrid method Distance matrix and approximate parsimony server J. Hein
PhyloQuart Quartet implementation (uses sequences or distances) Quartet method download V. Berry
MrBayes Posterior probability estimation Bayesian inference download J. Huelsenbeck et al.

Wikipedia does not yet have an article with this exact name. ... Clustal is a widely used multiple sequence alignment computer program. ...

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