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