XiaLab at University of Ottawa

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My software in bioinformatics and molecular evolution

These are software packages free for all. I generally answer user queries within two days, but will offer immediate feedback if you use the software for teaching.

  • DAMBE (Software package for extensive Data Analysis in Molecular Biology and Evolution, for Windows/MAC/Linux)

  • ARSDA (A comprehensive software package for analyzing RNA-Seq data (for 64-bit Windows with 32+ GB of RAM). Here is the Quick Start Guide.

  • PGT (High-quality mapping of a phylogeny onto a geographic region using either Bing Maps or Google Maps, with regular or satellite maps)

  • TRAD (Tip-Rooting and Ancestor-Dating)

  • PICs (Procrustes analysis of Image Configurations for Windows, with simple but intuitive online help.)

  • AMIADA (Analyzing Microarray Data, for Windows)

  • Two R scripts for JC69 with or without continuous gamma-distributed rates. They are plain text files that can be copied and pasted into an R window to evaluate the specified 4-OTU tree, and should be useful for teaching and exploring likelihood methods in phylogenetics.
    • New2.R assumes a constant rate over sites and estimates branch lengths for the star tree (with four branches) and a re-solved tree (with five branches).
    • NewGamma3.R implements a continuous gamma-distributed rate over sites for JC69, otherwise it is the same as New2.R
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