High Level modules for the Low Level Phylogenetic Likelihood Library
PLL-Modules depends on the PLL library submodule (libs/libpll), so you have to clone the repository as follows:
git clone --recursive https://github.com/ddarriba/pll-modulesor
git clone https://github.com/ddarriba/pll-modules
git submodule update --init --recursive
To compile and install module with the bundled version libpll, run:
./install-with-libpll.sh [TARGET_DIR]Alternatively, if you want to use a different version of libpll, you can run:
./autogen.sh
./configure CPPFLAGS="-Ipath/to/libpll" LDFLAGS="-Lpath/to/libpll"
make
make install # as root, otherwise run: sudo make installThe library will be installed on the operating system's standard paths. For
some GNU/Linux distributions it might be necessary to add that standard path
(typically /usr/local/lib) to /etc/ld.so.conf and run ldconfig.
Microsoft Windows compatibility was tested with a cross-compiler and seems to work out-of-the-box using MingW.
PLL-Modules is documented with Doxygen. Run the following command to generate the API description in HTML and LaTeX formats:
doxygen doxy.cfgAfterwards, the html API documentation is available at doc/html/index.html.
Additionally, you can generate pdf documentation by compiling the LaTeX output:
cd doc/latex
makePlease refer to the wiki page and/or the examples directory.
Please refer to the wiki page.
Below is a list of available modules in the current version. Check each individual README.md file in the correspondent subdirectory for more information.
| Module | Prefix | Description |
|---|---|---|
| binary | pllmod_bin_ | Binary I/O |
| msa | pllmod_msa_ | MSA management |
| optimize | pllmod_opt_ | Optimization algorithms |
| tree | pllmod_tree_ | Tree management |
| util | pllmod_util_ | Convenience functions |
| algorithm | pllmod_algo_ | High level algorithms |