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Reconstruction of ancestral genome maps
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README.md

ANGES 1.01, reconstructing ANcestral GEnomeS maps

Program: July 2012.

Documentation: August 2014 (v2)

Contact: Cedric Chauve (Dept. Mathematics, Simon Fraser University), cedric.chauve@sfu.ca

1. WHAT IS ANGES?

ANGES is a suite of Python scripts aimed at reconstructing ancestral genome maps from conserved genomic segments in extant genomes, including ingroups and outgroups.

ANGES takes for minimal input (1) a species tree describing the relationship between a group of extant genomes and with a marked ancestral node (the ancestor) and (2) a set of homologous markers (the markers) in the considered extant genomes. It computes conserved genomic segments between pair of species (the Ancestral Contiguous/Consecutive Sets, ACS), weights them according to their pattern of conservation in the extant genomes and combines these ACS into a set of ancestral chromosomal segments using a combinatorial framework that was widely used for computing physical maps, the Consecutive-Ones Property (C1P).

ANGES can reconstruct both multichromosomal linear ancestral genome maps (for eukaryotic genomes) and unichromosomal circular ancestral genome maps (for prokaryotic genomes).

ANGES can handle a wide variety of sets markers, obtained from gene families trees or multiple whole-genome alignments. It uses several combinatorial models of ACS, together with efficient algorithms for detecting them in pairs of genomes. It also uses several algorithms related to the C1P, from fast heuristics to exact branch-and-bound.

The methodological principles of ANGES have been described in the following papers.

C. Chauve, E. Tannier. A methodological framework for the reconstruction of contiguous regions of ances- tral genomes and its application to mammalian genomes. PLoS Computational Biology 4(11):e1000234, 2008

C. Chauve, H. Gavranovic, A. Ouangraoua, E. Tannier. Yeast ancestral genome reconstructions: the possibilities of computational methods II. Journal of Computational Biology 17:1097–1112, 2010.

H. Gavranovic, C. Chauve, J. Salse, E. Tannier. Mapping ancestral genomes with massive gene loss: A matrix sandwich problem Bioinformatics 27:i257–i265, 2011.

C. Chauve, J. Manuch, M. Patterson, R. Wittler. Tractability results for the consecutive-ones property with multiplicity. In CPM 2011, Lecture Notes in Comput. Sci. 6661:90–103, 2011.

2. INSTALLING ANGES.

ANGES is composed of a set of Python scripts, located in the src directory, and nothing needs to be done for its installation.

ANGES has been developed and tested on Unix (including Linux and MacOS) systems, using Python (http://www.python.org/) version 2.7.1+, with the numpy library (http://numpy.scipy.org/) and the Tkinter library for the graphical interface (http://wiki.python.org/moin/TkInter).

3. USING ANGES.

With the graphical interface: python src_path/MASTER/anges_CAR_UI.py

Without the graphical interface: python src_path/MASTER/anges_CAR.py parameter_file

In both cases, src_path is the path to access the ANGES source code.

Detailed instructions are provided in the manual anges_1.0.pdf and in the README files in the examples directories.

4. DIRECTORY STRUCTURE.

src: directory containing the python code

examples: a few examples using real data

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