A list of software for finding V, D, and J genes in observed repertoires and annotating junctions between germline genes and insertion regions.
This is a wiki page. Please edit and add software you know about. However, note that this is not the place for closed-source commercial software vendors to advertise their products.
Dedicated aligners
- BRILIA (Lee et al. 2017)
- CloAnalyst (Kepler 2013)
- Decombinator (Thomas et al. 2013) : uses a finite state automaton
- iHMMune-align (Gaeta et al. 2007) : Hidden Markov Model
- IgBLAST (Ye et al 2013) : highly tuned BLAST
- IgSCUEAL (Frost et al 2015) : phylogenetic placement
- IMSEQ (Kuchenbecker et al 2015)
- Joinsolver (Souto-Carneiro et al. 2004) : webserver only
- MiXCR (Bolotin et al 2015)
- partis, also ighutil (Ralph and Matsen 2016)
- repgenHMM (Elhanati et al. 2015)
- SoDA (binary available in Automation) (Volpe et al. 2006; see also Munshaw and Kepler 2010)
- VDJFasta (Glanville et al. 2009)
- VDJsolver (Ohm-Laursen et al. 2006)
Alignment wrappers and webservers
- Change-O (Gupta et al. 2015)
- IMGT V-QUEST (Lefranc et al 2008)
- ImmuneDB (Rosenfeld et al. 2017) : implements alignment method described in (Zhang et al. 2015)
- SONAR (Schramm et al. 2016)
- VBASE2 (Retter et al. 2004)