Archives

Coinfinder: a tool for the identification of coincident (associating and dissociating) genes in pangenomes.

What is it? Coinfinder is an algorithm and software tool that detects genes which associate and dissociate with other genes more often than expected by chance in pangenomes. Coinfinder is written primarily in C++ and is a command line tool which generates text, gexf, and pdf outputs for the user. Coinfinder uses a Bonferroni-corrected Binomial […]

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TIGER: Identifying rapidly-evolving characters in evolutionary data.

TIGER: Identifying rapidly-evolving characters in evolutionary data. About TIGER TIGER is open source software for identifying rapidly evolving sites (columns in an alignment, or characters in a morphological dataset). It can deal with many kinds of data (molecular, morphological etc.). Sites like these are important to identify as they are very often removed or reweighted […]

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CLANN: Software for inferring phylogenetic supertrees.

CLANN: Software for inferring phylogenetic supertrees. What is clann? Clann (the Irish word for “family”), is a free software program designed and written by Chris Creevey at the Bioinformatics and Molecular Evolution Unit at NUI Maynooth. The purpose of the program is to implement methods of determining the optimal phylogenetic supertree, given a set of […]

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ModelGenerator: amino acid and nucleotide substitution model selection

ModelGenerator is a a free, easy-to-use model selection program, designed and written by Thomas Keane, that selects optimal amino acid and nucleotide substitution models from Fasta or Phylip alignments. ModelGenerator supports 56 nucleotide and 96 amino acid substitution models. Modelgenerator uses the Akaike Information Criterion (AIC), the Bayesian Information Criterion (BIC) and hierarchical Likelihood-ratio tests […]

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CRANN: Software for inferring selection

CRANN Crann (pronounced ‘crown’) is the Irish word for ‘tree’. The program Crann has been developed in order to provide fast heuristic methods of detecting adaptive evolution in protein-coding genes. It is important that the user understands the advantages and limitations of these methods. It is also important for the user to know that the […]

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PutGaps : DNA gapped file from Amino Acid alignment

PutGaps : DNA gapped file from Amino Acid alignment Copyright © David Fitzpatrick, Melissa Pentony 2004 PutGaps is a free software program designed and written by David Fitzpatrick and Melissa Pentony. The purpose of the program is to add gaps to a DNA alignment file based on its Amino Acid equivalent. PutGaps has been written […]

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GCUA: General Codon Usage Analysis

GCUA: General Codon Usage Analysis GCUA was initially written while working at the Natural History Museum, London. The pdf describing the program can be downloaded here. You can find the project on GitHub here: https://github.com/mcinerneylab/GCUA Purpose: This program is designed to perform various tasks that are of use for evaluating codon usage in a set of genes.  You […]

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