pamlX: A Graphical User Interface for PAML
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Yang et al. as mentioned in this paper present pamlX, a graphical user interface/front end for the paml (for Phylogenetic Analysis by Maximum Likelihood) program package.Abstract:
This note announces pamlX, a graphical user interface/front end for the paml (for Phylogenetic Analysis by Maximum Likelihood) program package (Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556; Yang Z. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591). pamlX is written in C++ using the Qt library and communicates with paml programs through files. It can be used to create, edit, and print control files for paml programs and to launch paml runs. The interface is available for free download at http://abacus.gene.ucl.ac.uk/software/paml.html.read more
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References
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Journal ArticleDOI
PAML 4: Phylogenetic Analysis by Maximum Likelihood
TL;DR: PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML), which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses.
Journal ArticleDOI
PAML: a program package for phylogenetic analysis by maximum likelihood
TL;DR: The strength of PAML, in comparison with other phylogenetic packages currently available, is its implementation of a variety of evolutionary models, which include several models of variable evolutionary rates among sites, models for combined analyses of multiple gene sequence data and models for amino acid sequences.
Journal ArticleDOI
Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference
TL;DR: A modification of the KH test to take into account a multiplicity of testings is presented, which shows how the test was designed for comparing two topologies but is often used for comparing many topologies.
Journal ArticleDOI
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea
Hirohisa Kishino,Masami Hasegawa +1 more
TL;DR: A new method for estimating the variance of the difference between log likelihood of different tree topologies is developed by expressing it explicitly in order to evaluate the maximum likelihood branching order among Hominoidea.