Software from my group
  • AMAP Protein multiple alignment
  • Cufflinks Transcript assembly and abundance estimation for RNA-Seq
  • FSA Fast Statistical Alignment
  • GENEMAPPER Reference based gene annotation
  • MAVID Multiple alignment of large genomic sequences
  • MERCATOR Homology mapping
  • MJOIN Neighbor joining with subtree weights
  • PARALIGN Alignment polytope construction
  • SLAM Pairwise simultaneous alignment and gene finding
  • SLIM Minimum network design for optimizing the search space for pair hidden Markov models
  • TopHat Splice junction mapper for short RNA-seq reads
  • VISTA Visualization tool for global alignments