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
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.
Readme file describing the usage of SWAPSC
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.
Readme file describing the usage of GRAST
CAPS 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coevolution as published in Genetics (Fares and Travers, 2006) but it also includes several other anayyses unpublished to date, such as the preliminary analysis of compensatory mutations and inter-protein coevolution analysis.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. 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.
Readme file describing the usage of CAPS
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.
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.
In this section you will find small scripts and programs that have been written to carry out small, very specific tasks that are done on a regular basis. These scripts usually are time saving devices that speed up or automate processes and sequences of processes - enabling complete reproducibility of analysis.
Software to split a sequence alignment into as many files as sequences