BppSuite presentation
BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis.
Installation
Standalone executables
Standalone executables are available for linux64
From source files
Get the sources
This is done with git, for example in directory $bpp_dir:
cd $bpp_dir
git clone https://github.com/BioPP/bppsuite
Compiling
Bio++ libraries need to be installed beforehand, for example in $bpp_dir. The needed libraries are bpp-core, bpp-seq, bpp-phyl, bpp-popgen.
After, you proceed:
cd bppsuite
cmake -DCMAKE_INSTALL_PREFIX=$bpp_dir ./ # prepare compilation
make # compile
make install # move files to the installation directory (this will create a $bpp_dir/bin/ directory)
That's it ! The executables are now installed in $bpp_dir/bin.
Without the option -DCMAKE_INSTALL_PREFIX=$bpp_dir, the standard /usr/local directory will be used, and the executables installed in /usr/local/bin, a location which requires superuser access rights.
Usage
Bppsuite executables should know where the dynamic libraries are. A way to check it is the command:
ldd $bpp_dir$/bin/bppml
To configure this, set in the shell environment variable :
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$bpp_dir
(and source the configuration file or relog).
Documentation
You can also generate the pdf documentation by typing :
make pdf
Examples
Many examples are available in the subdirectory of Examples.
Documentation
Documentation can be found in one page at: http://bioweb.me/bppsuite-doc
Or on github: https://github.com/BioPP/bppsuite/releases/tag/v2.3.2 in pdf or html.