Evolutionary tools for genomic analysis
| AIS | Almost Invariant Sets |
| ALVIS | Interactive non-aggregative multiple sequence ALignment VISualisation |
| AYB | Base calling software for the Illumina GA platform |
| BOSS-RUNS | Benefit-Optimising Short-term Strategy for Read Until Nanopore Sequencing |
| EDIBLE | Experimental Design and Information By Likelihood Exploration. |
| KAV | KAlignmentViewer – an interface for the display and browsing of multiple sequence alignments – is no longer distributed or supported |
| MAPLE | MAximum Parsimonius Likelihood Estimation |
| 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 |
| PEAR | Phylogeny Embedding & Approximate Representation |
| phastSim | fast phylogenetic simulator |
| 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 |