BioClojure is an open-source library for the manipulation of biological sequence data written in the language Clojure. BioClojure aims to provide a functional framework for the processing of biological sequence data that provides simple mechanisms for concurrency and lazy evaluation of large datasets.
scrm (sequential coalescent with recombination model ) is a coalescent simulator for biological sequences. Different to similar programs, it can approximate the Ancestral Recombination Graph as closely as needed, but still has only linear runtime cost for long sequences. It allows you to rapidly simulate chromosome scale sequences with essentially correct genetic linkage.
PANOW (Poisson Approximation for the Number of Occurrences of Words)is a software dedicated to the search of rare words in biological sequences (over- or under-represented words in DNA or protein sequences).
Sirius PSB (Sirius Prediction System Builder) is a software to carry out sequence (DNA or protein) analysis. Main operations: 1) Building a classifier 2) Deploying a classifer 3) Search for proteins similar to query proteins 4) Preliminary and post prediction analysis (Visualization)