AISAlmost Invariant Sets
ALVISInteractive non-aggregative multiple sequence ALignment VISualisation
AYBBase calling software for the Illumina GA platform
EDIBLEExperimental Design and Information By Likelihood Exploration.

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

PANDITPANDIT database of alignments and trees of Protein and Associated Nucleotide Domains with Inferred Trees
PASSMLPhylogeny and Secondary Structure using Maximum Likelihood.
pcrcoal R package for coalescent simulations of PCR
PhyloSim Monte Carlo simulation of sequence evolution
PRANKProbabilistic Alignment Kit
webPRANKWeb server for PRANK sequence alignment
RATSResource Aware Taxon Selection
rlsimrlsim collection of tools for simulating RNA-seq
RNAcodeAnalysis of protein coding potential in multiple sequence alignments
SLRSitewise Likehood Ratio estimation of selection
simNGSSimulating observations from Illumina NGS machines