codonPhyML

codonPhyML uses Markovian codon models of evolution in phylogeny reconstruction. Given a set of species characterized by their DNA sequences as input, codonPhyML will return the phylogenetic tree that best describes their evolutionary relationship. Our paper describing codonPhyML has been published in the journal "Molecular Biology and Evolution" (MBE). For more details, follow the link: http://mbe.oxfordjournals.org/content/30/6/1270. codonPhyML is on the cover of MBE! Check this out (August 2013): http://mbe.oxfordjournals.org/content/30/8.toc.

For the multimodel version of CodonPhyML, please use the 'codonphyml_multi.tgz' tarball.

Features

Markovian codon models of evolution: Goldman & Yang 1994, Muse & Gaut 1994, Kosiol et al 2007, Schneider et al 2005, Yap et al 2010
NNI and SPR tree topology search heuristic
substitution rate parameters estimated by maximum likelihood
multicore support through OpenMP
likelihood comparable across different models (i.e. AA, NT and CODON)

Project Samples

MBE issue featuring codonPhyML on the cover

Project Activity

See All Activity >

License

GNU General Public License version 3.0 (GPLv3)

Follow codonPhyML

codonPhyML Web Site

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Additional Project Details

Operating Systems

BSD, Linux, Windows

Languages

English

Intended Audience

Education, Science/Research

User Interface

Command-line, Console/Terminal

Programming Language

Related Categories

C Bio-Informatics Software

Registered

2010-10-09

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