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# libpll-2 | ||
# # Libpll-2 | ||
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libpll-2 is the new official fork of libpll (https://github.com/xflouris/libpll/). It implements site repeats to speed up computations. | ||
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Please read the wiki for more information. | ||
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# 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](https://github.com/amkozlov/raxml-ng): speedup ranges between 1.2 and 1.5 | ||
* [ModelTest-NG](https://github.com/ddarriba/modeltest): speedup around 1.3 | ||
* [EPA-ng](https://github.com/Pbdas/epa-ng): memory footprint reduced by 30%. | ||
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# Compilation instructions | ||
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Currently, `libpll` requires that [GNU Bison](http://www.gnu.org/software/bison/) | ||
and [Flex](http://flex.sourceforge.net/) are installed on the target system. On | ||
a Debian-based Linux system, the two packages can be installed using the command | ||
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`apt-get install flex bison` | ||
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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. | ||
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The library can be compiled using either of the following two ways. | ||
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**Cloning the repo** Clone the repo and bild the executable and documentation | ||
using the following commands. | ||
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```bash | ||
git clone https://github.com/xflouris/libpll.git | ||
cd libpll | ||
./autogen.sh | ||
./configure | ||
make | ||
make install # as root, otherwise run: sudo make install | ||
``` | ||
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When using the cloned repository version, you will also need | ||
[autoconf](https://www.gnu.org/software/autoconf/autoconf.html), | ||
[automake](https://www.gnu.org/software/automake/) and | ||
[libtool](https://www.gnu.org/software/libtool/) installed. On a Debian-based | ||
Linux system, the packages can be installed using the command | ||
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```bash | ||
sudo apt-get install autotools-dev autoconf libtool | ||
``` | ||
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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`. | ||
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Microsoft Windows compatibility was tested with a cross-compiler and seems to | ||
work out-of-the-box using [MingW](http://www.mingw.org/). | ||
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# libpll-2 license and third party licenses | ||
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The libpll-2 code is currently licensed under the | ||
[GNU Affero General Public License version 3](http://www.gnu.org/licenses/agpl-3.0.en.html). | ||
Please see LICENSE.txt for details. | ||
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libpll-2 includes code from several other projects. We would like to thank the | ||
authors for making their source code available. | ||
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libpll includes code from GNU Compiler Collection distributed under the GNU | ||
General Public License. | ||
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The future line of libpll... |
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