PAML: a program package for phylogenetic analysis by maximum likelihood

摘要: PAML, currently in version 1.2, is a package of programs for phylogenetic analyses DNA and protein sequences using the method maximum likelihood (ML). The can be used (i) estimation evolutionary parameters such as branch lengths tree, transition/transversion rate ratio, shape parameter gamma distribution variable rates at sites, different genes; (ii) ratio test hypotheses concerning sequence evolution, constancy independence among sites lineages (the molecular clock); (iii) calculation substitution reconstruction ancestral nucleotide or amino acid sequences; (iv) tree by Bayesian methods. strength comparison with other packages available, its implementation variety models. These include several models combined multiple gene data sequences. Multifurcating trees are supported, well which some to others. A heuristic search algorithm (star decomposition) package, but making not strong point current version, although work under way implement efficient algorithms. Major types they perform, listed Table 1. More details available documentation included written Microsoft Word. PAML distributed free charge academic use only. including ANSI C source codes, documentation, example sets, control files, obtained anonymous ftp mw511.biol.berkeley.edu/pub, from Indiana biology site ftp.bio.indiana.edu directory Incoming molbio/evolve . MAC PowerMac executables also DOS prepared yet. Further information about World Wide Web