- Software developed in the Pachter group and still under active development in the group
- Software developed in the Pachter group but now maintained/developed elsewhere
- SWALO (2016) Scaffolding with assembly likelihood optimization (now supported by Atif Rahman)
- PROBer (2015) Quantitative modeling of transcriptome-wide RNA structure-probing experiments (now supported by Bo Li)
- CGAL (2013) Computing genome assembly likelihoods (now supported by Atif Rahman)
- FSA (2009) Fast Statistical Alignment (now supported by Robert Bradley and his group at FHCRC)
- MERCATOR (2004) Homology mapping (now supported by Colin Dewey and his group at the University of Wisconsin)
- Retired Software
These programs, originally developed in the Pachter group, are no longer under active development and are not being supported.
- eXpress (2012) Streaming quantification for high-throughput sequencing (recommended instead: kallisto)
- SysCall (2011) Distinguishing heterozygous sites from systematic error in high-thoughput sequenced reads (archived here)
- ReadSpy (2012) Assessment of uniformity in RNA-Seq reads
- MetMap (2010) Analysis of Methyl-Seq experiments
- Cufflinks (2010) Transcript assembly and abundance estimation for RNA-Seq (recommended instead: kallisto and sleuth)
- Tophat (2009) Splice junction mapper for short RNA-seq reads (archived here)
- AMAP (2007) Protein multiple alignment
- GENEMAPPER (2006) Reference based gene annotation (recommended instead: an RNA-Seq experiment)
- MJOIN (2006) Neighbor joining with subtree weights
- PARALIGN (2006) Alignment polytope construction
- SLIM (2003) Minimum network design for optimizing the search space for pair hidden Markov models
- SLAM (2003) Pairwise simultaneous alignment and gene finding (recommended instead: an RNA-Seq experiment)
- MAVID (2003) Multiple alignment of large genomic sequences
- VISTA (2000) Visualization tool for global alignments
