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Phylogenetic Sampling and Optimization of Sequence Alignments

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PhySamp is a package dedicated to phylogenetic sampling. It samples a sequence alignment according to its corresponding phylogenetic tree. Current stable version is 0.2.0. Current development version is 1.0.0, and works with the development version of Bio++ (2.3.0).


The PhySamp package currently contains two programs:


The bppalnoptim and bppphysamp programs are command-line driven. You can get pre-compiled executable files for your system for the stable version. Stable and development versions can be compiled on any system with a decent C++ compiler (include at least Linux and MacOS). The latest version of PhySamp (0.2.0) is based on Bio++ 2.2.0, also available on GitHub Development version is 1.0.0, and is based on the development version of Bio++.

The programs depend on the Bio++ libraries. Pre-compiled executables are statically linked, and therefore already include all required code from the libraries. Pre-compiled packages will ask for all required dependencies, which can be found in the same download directory. For compiling the programs yourself, from the downloaded sources or from the git repository, please follow the instructions from the Bio++ website


Several example data sets are distributed along with the source code of the package. A reference manual is also available here, or can be downloaded as PDF. Questions can be asked on the dedicated forum: here.