Software



Software applications that have been developed as part of the research carried out at this lab are available for download here. All software is freely available and distributed under the terms of the GNU Pubic License Agreement (Version 3). A copy of the agreement can be found here

Sliding Window Analysis Procedure to detect Selective Constraints (SWAPSC)
swapsc.tar.gz
SWAPSCv1.0 is the first version of the Sliding Window Analysis Procedure to detect Selective Constraints in protein-coding genes. The software was previously written in PERL (2002). The large amount of information data generated and the exhaustive screening algorithm of selective constraints required the performance of a more friendly and easy-to-run software.This software include an automatic windowing screening for selective constraints and the Kimura's method of Li (1993) to compare synonymous and non-synonymous nucleotide estimated substitution rates with those expected under neutrality.
swapscreadme.pdf
Readme file describing the usage of SWAPSC
grast.tar.gz
Genome Reduction Analysing Software Tool (GRAST). GRAST allows the user to analyse genome reduction by whole genome comparison between a reduced genome and a reference genome (a close relative to the reduced genome). A number of the options in GRAST can also be used for a whole genome comparison of non-reduced genomes.
grastreadme.pdf
Readme file describing the usage of GRAST

Clustering Analysis of Functional Shifts (CAFS)
cafs_src.zip
cafs1.0_mac10.6.zip
cafs1.0_linux.zip(any bugs here should be fixed now)
cafs user manual
This is the first version of CAFS. This program analyses alignments and provides the user with the best putative sites under functional divergence.

Coevolution Analysis using Protein Sequences (CAPS)



CAPSv2.0

caps2.0_src.zip
caps2.0_mac-64-bit.zip
caps2.0_mac10.6.zip
caps2.0_mac10.5.zip
caps2.0_linux_x86_64-bit.zip
caps2.0_linux_x86_32-bit.zip
caps_manual.pdf
is the second version of the software aimed at measuring the coevolution between amino acid sites belonging to the same protein(intra-molecular coevolution) or to two functionally or physically interacting proteins (inter-molecular coevolution). The Software implements an improved method to detect intra-molecular coevolution as published in Genetics (Fares and Travers, 2006) and also inter-protein coevolution analysis. The improved scoring of amino acid sites is obtained by maximum likelihood ancestral state reconstruction along with simulations to assess significance. In addition to these improvements we also implement a test which assesses whether two proteins are interacting. This version is provided in C++ with both source code and binary distributions for a number of popular operating systems. This update also represents a significant speed increase on the previous version.

CAPSv1.0
capsunix.tgz
CAPS 1.0 is the first version of the software aimed at measuring the coevolution between amino acid sites belonging to the same protein(intra-molecular coevolution) or to two functionally or physically interacting proteins (inter-molecular coevolution). The Software implements the method to detect intro-molecular coevolution as published in Genetics (Fares and Travers, 2006) but it also includes several other anayyses unpublished to date, such as the preliminary analysis of compensatory mutations and inter-protein coevolution analysis. New modules have been introduced to conduct preliminary analyses of compensatory mutations. These analyses include the detection of correlation in the evolution of hydrophobic or molecular weight characteristics of two amino acid sites in a multiple sequence alignment. Further, unlike the previous Beta versions developed to detect intra-molecular coevolution by implementing the method Fares and Travers (2006), this first released version includes other analyses that permit the identification of inter-molecular coevolution and the inference of protein-protein functional interactions.
capswindows.tgz
capsreadme.pdf
Readme file describing the usage of CAPS

CAPSv1.0 server
A Web-based version of CAPS (CAPS Server) is now available for your convenience. This application is based on CAPS Version 1.0 and also uses the newly developed Coevolution Visualization Tools to generate images that highlight co-evolving amino acids.
coevolution_darwin.tgz
For the visualization of coevolving amino acids two programs were developed: 1. coevolution is a program that creates a 'ball-and-sticks' model; 2. structure generates a more realistic image using the 3-D structure in PDB format. These tools are being used by CAPS Server for generating snapshots that are part of the results output. You can download their source code, which was written in C++ and compile it under any environment that supports the OpenSceneGraph tool kit. For Windows XP a binary version is provided. Together with the input files generated by CAPS Server you can then explore your protein and the co-evolving amino acids more interactively, i.e. zoom in and out and rotate an image. The programs have been developed by Miguel Angel Gamon at the University of Valencia under supervision of Dr. Mario Fares.
coevolution_win.zip

New Publications:

1. Williams TA, Codoñer FM, Toft C, Fares MA. Two chaperonin systems in bacterial genomes with distinct ecological roles. Trends Genet. 2010 Feb;26(2):47-51. Epub 2009 Dec 28
2. Garceau V, Smith J, Paton IR, Davey M, Fares MA, Sester DP, Burt DW, Hume DA. Pivotal Advance: Avian colony-stimulating factor 1 (CSF-1), interleukin-34 (IL-34), and CSF-1 receptor genes and gene products. J Leukoc Biol. 2010 Jan 5. [Epub ahead of print]
3. Jiang X, Fares MA. IDENTIFYING COEVOLUTIONARY PATTERNS IN HUMAN LEUKOCYTE ANTIGEN (HLA) MOLECULES. Evolution. 2009 Nov 20. [Epub ahead of print]