AWTY
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- Spectronet
- rwty
- PRALINE
- YACOP
- rBiopaxParser
- Consed
- STRAP
- STRait Razor
- AMoRe
- MOLREP
- Coot
- GFF-Ex
- RamiGO
- kClust
- CLAP
- EVEREST
- CATH
- HAMAP
- PIRSF
- FunTree
- Gene3D
- M-Coffee
- SEAVIEW
- PHYLO_WIN
- Cgaln
- FRESCO
- BRIG
- CGView
- Dotlet
- JDotter
- M-GCAT
- AceView
- GtRNAdb
- Savant Genome Browser
- MEME-LaB
- piRNABank
- piRBase
- piRNAQuest
- ModuleMaster
- MATCH
- Stampy
- NextGenMap
- Ensembl REST
- BioStar
- TICO
- CRITICA
- ZCURVE
- MOCAT
- GOLD
- Conrad
- CONTRAST
- mGene
- REGANOR
- jModelTest
- PhyloBayes 3
- SeqVis
- LDDist
- BMGE
- CLANN
- TOPAL
- Tracer
- Bayesian modelling of compositional heterogeneity in molecular phylogenetics
- Bioinformatics. Volume I. Data, sequence analysis, and evolution
- Visualizations for assessing convergence and mixing of Markov chain Monte Carlo simulations
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