Software developed in the Pachter group and still under active development in the group
  • sleuth (2015) RNA-Seq differential analysis
  • kallisto (2015) RNA-Seq quantification
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)
  • VISTA (2000) Visualization tool for global alignments (now supported by Inna Dubchak and her group at the JGI)
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 (recommended instead: FSA)
  • GENEMAPPER (2006) Reference based gene annotation (recommended instead: an RNA-Seq experiment)
  • MJOIN (2006) Neighbor joining with subtree weights (archived here)
  • PARALIGN (2006) Alignment polytope construction (archived here)
  • SLIM (2003) Minimum network design for optimizing the search space for pair hidden Markov models (archived here)
  • SLAM (2003) Pairwise simultaneous alignment and gene finding (recommended instead: an RNA-Seq experiment)
  • MAVID (2003) Multiple alignment of large genomic sequences (recommended instead: FSA)