Seqotron: Alignment editor for Mac OS X written in Objective-C/Cocoa that is supposed to replace the famous Se-Al program that does not run on OS X > 10.7. This is a pre-alpha release and has limited functionalities. It will eventually be distributed as open source software.

Physher: C program to infer evolutionary rates and divergence times using genetic data.

Patristic: Java program that uses as input different tree files and computes their patristic distances.

Virusbanker: MySQL database of virus sequences and alignments that is accessed via a Java program.

iConvert.pl: Perl script converting tree files and sequence files between common formats . This program supports FASTA, PIR, Clustal and Nexus sequence files and Phylip, Nexus, Clustal tree files.

modeltest.pl: Perl script using PHYML (Guindon and Gascuel, 2003) to compute AIC, BIC and hLRT for the selection of a DNA and amino acid model. It uses the functions from the original ModelTest to compute the hLRT (Posada and Crandall, 1998).

SWeBLAST (Sliding Window Web-based BLAST): Perl program that looks for recombinations in non-aligned sequences using BLAST. (SWeBLAST: a Sliding Window Web-based BLAST tool for recombinant analysis. J Virol Methods. 2008, 152, 98-101)

DnDscan: Perl implemention of the DnDscan program described in: Gibbs MJ, Wayper P, Fourment ML, Wood JT, Ohshima K, Armstrong JS, Gibbs AJ. The variable codons of H3 influenza A virus haemagglutinin genes. Arch Virol. 2007 Jan;152(1):11-24

Siscan linux Windows mac: C program for detecting recombination in a set of aligned DNA or amino acid sequences.

Test of saturation R script: Test of saturation based on the Xia and Xie method. The script reads in frame DNA sequences in FASTA format. Both transitions and transversions are plotted against evolutionary distances calculated with the JC69 model. The output consists of several plots saved in the pdf format.

HyPhy language plugins for TextWrangler and Xcode.

Uncertainty plot R script. Use multidimensional scaling to plot the uncertainty of phylogenetic trees using posterior samples of trees calculated using BEAST. Several genes can be loaded in order to assess differences in evolutionary histories. More comments are available in the source code.

Patristic distances for sets of trees mac. Can be used for the uncertainty plot. Input: a text file with tree file names and their respective burnins (see example file). Output patristic distances, each line represents all the distances of one tree. A column will contain the distances between the same pair of nodes across all the trees.