Topological inference of horizontal evolution from multiple sequence alignments
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TARGet
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README.md

TARGet

TARGet is a light-weight application for reconstructing non-vertical evolutionary histories from sampled genetic sequences. It makes use of persistent homology, a tool from topological data analisys, to infer information about the minimal set of reticulate events (recombination, re-assortment, etc) that are needed to explain a sequence alignment, under the assumption of no convergent evolution.

It requires the following free software in the system:

  • Python 2.7 (Python 3 is currently not supported.)
  • CMake
  • Boost C++ libraries, including Boost.Python
  • NetworkX package for Python.

For optimal visualization results it is recommended to have Graphviz tools and PyGraphviz installed, although they are not strictly required.

Once the above dependences are installed in the system, unpack and build TARGet by typing the following commands in a terminal:

tar -xvzf TARGet.tar.gz

cd TARGet

mkdir build

cd build

cmake ..

make

  • On Mac OSX, CMake often has issues finding the correct python path. If that is the case, uncomment the following three lines in file CMakeLists.txt, replacing the directories for the appropriate ones in your system,

set (PYTHON_EXECUTABLE /usr/local/bin/python2.6)

set (PYTHON_INCLUDE_DIR /usr/local/include/python2.6)

set (PYTHON_PATH /usr/local/lib/libpython2.6.dylib)

and run cmake and make again.

  • Some compiler versions may raise the following error:

error: unrecognized command line option "-ftemplate-depth=256"

If that is the case, replace the following line in CMakeList.txt,

add_definitions (-ftemplate-depth=256)

by,

add_definitions (-ftemplate-depth-256)

and run cmake and make again.

  • It is important to run TARGet using the same version of Python that was used to compile TARGet and Boost libraries.

TARGet executable is in directory TARGet. You can check that TARGet has been correctly installed by running it on any of the test or the example FASTA files that come with the distribution, e.g.:

./TARGet test.fa

or

python TARGet test.fa

A detailed description of TARGet is found in the file docs/Manual.pdf.

TARGet is distributed under the GNU General Public License (GPL v3). A copy of license is included in the file Copying.txt.

This program heavily relies on Dmitriy Morozov's Dionysus C++ library for persistent homology computations, the relevant parts of which are distributed together with TARGet also under the terms of GPLv3 license.

If you use TARGet in your research, please include in your reference list the following publication:

Camara, P.G., Levine, A.J. and Rabadan, R. (2015), "Inference of ancestral recombination graphs through topological data analysis". arXiv:1505.05815.