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The main tool in this package builds phylogenies under the maximum likelihood criterion. It implements a large number of substitution\nmodels coupled to efficient options to search the space of phylogenetic tree topologies. PhyTime is another tool in the PhyML package that focuses\non divergence date estimation in a Bayesian setting. The main strengths of PhyTime lies in its ability to accommodate for uncertrainty in the placement of fossil calibration\nand the use of realistic models of rate variation along the tree. Finally, PhyREX fits the spatial-Lambda-Fleming-Viot\nmodel to geo-referenced genetic data. This model is similar to the structured coalescent but assumes that individuals are distributed along a spatial continuum rather\nthan discrete demes. PhyREX can be used to estimate population densities and rates of dispersal. Its output can be processed by treeannotator (from the BEAST package) as well as\nSPREAD.\n\n### Citations\n\n- New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0 S Guindon, JF Dufayard, V Lefort, M Anisimova, W Hordijk, O Gascuel *Systematic Biology* 59 (3), 307-321, 2010.\n- Accounting for calibration uncertainty: Bayesian molecular dating as a “doubly intractable” problem S Guindon *Systematic Biology* 67 (4), 651–661, 2018.\n- Demographic inference under the coalescent in a spatial continuum S Guindon, H Guo, D Welch *Theoretical Population Biology* 111, 43-50, 2016.\n\n\n### Installation\n\nTo install any program that is part of the PhyML package, type the following command:\n\n```bash\nsh ./autogen.sh;\n```\n\nIf you are using a Mac computer or running a Unix-like operating system, you will need \nto install the packages autoconf automake and pkg-config. On a Mac, the following command \nshould set you up (provided Homebrew is installed on your Mac...): brew install pkg-config\nautoconf automake;\n\nNext, to install any program that is part of the PhyML package, type the following commands:\n\n```bash\n./configure --enable-XXXX;\nmake;\n```\nwhere XXXX is phyml or phyrex or phytime.\n\nTo compile a Windows executable, install MinGW and run:\n\n```bash\n./configure --enable-win --enable-XXXX;\nmake;\n```\n\nTo install the MPI version of PhyML, type the following commands:\n\n```bash\nautoreconf -i;\n./configure --enable-phyml-mpi;\nmake;\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstephaneguindon%2Fphyml","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstephaneguindon%2Fphyml","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstephaneguindon%2Fphyml/lists"}