Our major and currently actively used programs are hosted at github at https://github.com/MikeAxtell . The most important and current ones are
- ShortStack : Alignment, annotation, and quantification of small RNAs
- CleaveLand4 : Analysis of degradome data to find sliced miRNA and siRNA targets
There are also lots of older scripts that we’ve used / referenced / released over the years. Some are on github at https://github.com/MikeAxtell and other can be found here. These however are older, not used, and not really supported by us anymore.