- AUGUSTUS - Gene prediction for eukaryotes using HMM
- UFO - Ultra-fast functional profiling of large protein sequence collections
- MarVis - Clustering and Visualization of Metabolic Markers
- jpHMM-HIV - Subtyping HIV-1 with a Jumping Profile Hidden Markov Model (jpHMM)
- Anchored DIALIGN - Multiple sequence alignment with user-defined constraints
- CHAOS-DIALIGN- Pair-wise and multiple alignment of genomic sequences
- DIALIGN-TX - Multiple Protein and DNA Alignment
- Dialign with secondary structure Multiple protein sequence alignment using secondary structure prediction
- TiCo - Postprosessing of gene predictions for prokaryotes
- ARGUS - Coalescent model with recombination for HIV classification
- Orphelia - predicting genes in metagenomic sequencing reads
- OrthoSelect - Selection of orthologs in phylogenomics
- TreePhyler - Fast taxonomic profiling of metagenomes
- Taxy
- Musi - Analysis of gene libraries generated by codon-directed mutagenesis