Download
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
Categories
Bio-InformaticsLicense
GNU General Public License version 3.0 (GPLv3)Follow codonPhyML
Other Useful Business Software
Demo Series - Small Business Backup By Veeam
Watch this on-demand demo series and learn how to protect your Microsoft 365 data with clear, simple, actionable steps that are easy to implement for businesses of all sizes.
Rate This Project
Login To Rate This Project
User Reviews
Be the first to post a review of codonPhyML!
