pombredanne / libpll-2

Phylogenetic Likelihood Library 2 - experimental

# Libpll-2

libpll-2 is the new official fork of libpll (https://github.com/xflouris/libpll/). It implements site repeats to speed up computations.

Please read the wiki for more information.

Projects that are already using libpll-2

List of projects already using libpll-2 and site repeats, and reported speedups compared with the tip pattern optimization:

• RAxML-NG: speedup ranges between 1.2 and 1.5
• ModelTest-NG: speedup around 2
• EPA-ng: no speedup (likelihood computation is not the main bottleneck) but memory footprint reduced by 30%.

Compilation instructions

Currently, libpll requires that GNU Bison and Flex are installed on the target system. On a Debian-based Linux system, the two packages can be installed using the command

apt-get install flex bison

The library also requires that a GNU system is available as it uses several functions (e.g. asprintf) which are not present in the POSIX standard. This, however will change in the future in order to have a more portable and cross-platform library.

The library can be compiled using either of the following two ways.

Cloning the repo Clone the repo and bild the executable and documentation using the following commands.

git clone https://github.com/xflouris/libpll.git
cd libpll
./autogen.sh
./configure
make
make install    # as root, otherwise run: sudo make install

When using the cloned repository version, you will also need autoconf, automake and libtool installed. On a Debian-based Linux system, the packages can be installed using the command

sudo apt-get install autotools-dev autoconf libtool

The 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.

libpll-2 license and third party licenses

The libpll-2 code is currently licensed under the GNU Affero General Public License version 3. Please see LICENSE.txt for details.

libpll-2 includes code from several other projects. We would like to thank the authors for making their source code available.

libpll includes code from GNU Compiler Collection distributed under the GNU General Public License.