This is the Linux app named codonPhyML whose latest release can be downloaded as codonPhyML_dev_1.00_201407.24.zip. It can be run online in the free hosting provider OnWorks for workstations.
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codonPhyML
DESCRIPTION
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)
Audience
Science/Research, Education
User interface
Console/Terminal, Command-line
Programming Language
C
This is an application that can also be fetched from https://sourceforge.net/projects/codonphyml/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
