This repository contains various analysis scripts for HyPhy -- a molecular evolutionary analysis platform.
git clone https://github.com/veg/hyphy-analyses.git hyphy-analyses
Unless otherwise stated in directory - specific README file, all analyses assume the availability of the HyPhy develop build. General steps for obtaining one on Linux and OS X systems and running an analysis-file, assuming you have
- C/C++ toolchains, like GCC or Clang
- CMake
is as follows
git clone https://github.com/veg/hyphy.git hyphy-develop
cd hyphy-develop
git checkout develop
cmake ./
make -j MP
#if you want a system-wide install...
make install
Now, you can run a specific standalone analysis or look for options
/path/to/hyphy /path/to/hyphy-analysis/module/analysis.bf --help
...
/path/to/hyphy /path/to/hyphy-analysis/module/analysis.bf --kw1 arg1 --kw2 arg2 ....
for example
cd /home/sergei/hyphy-analyses/codon-msa
hyphy pre-msa.bf --input example.fas
Specific analysis directories have more specific analysis options and examples.