AIS Almost Invariant Sets
ALVIS Interactive non-aggregative multiple sequence ALignment VISualisation
AYB Base calling software for the Illumina GA platform
EDIBLE Experimental Design and Information By Likelihood Exploration.

KAlignmentViewer - an interface for the display and browsing of multiple sequence alignments - is no longer distributed or supported

PANDIT PANDIT database of alignments and trees of Protein and Associated Nucleotide Domains with Inferred Trees
PASSML Phylogeny and Secondary Structure using Maximum Likelihood.
pcrcoal  R package for coalescent simulations of PCR
PhyloSim  Monte Carlo simulation of sequence evolution
PRANK Probabilistic Alignment Kit
webPRANK Web server for PRANK sequence alignment
RATS Resource Aware Taxon Selection
rlsim rlsim collection of tools for simulating RNA-seq
RNAcode Analysis of protein coding potential in multiple sequence alignments
SLR Sitewise Likehood Ratio estimation of selection
simNGS Simulating observations from Illumina NGS machines