Software

Here are some software packages developed by my group:

• Armatus - multi-scale topological domain detection from Hi-C data.
• MINCE - reference-free compression of short-read sequencing data.
• Salmon - fast, accurate isoform abundance estimation from RNA-seq data (spiritualy Sailfish 2.0).
• PathEnc - Reference-based compression of short read data sets.
• Sailfish - ultrafast isoform abundance estimation from RNA-seq reads.
• PARANA 2 - parsimonious estimates of ancestral networks.
• CORAL - system for interactive visualizations of differences between clusterings.
• Map of Jazz Musicians - web application to explore recorded collaborations between jazz musicians.
• GiRaF - find reassortments in collections of influenza genome sequences.
• JELLYFISH - count k-mers in large sequence databases very fast.
• PARANA - parsimonious reconstruction of ancestral interaction networks.
• GHOST - Global alignment between two graphs.
• STARFISH - Identify rigid components with the pebble game and a body-bar-and-hinge reduction
• TransTermHP - find rho-independent transcription terminators in bacterial genomes.
• Network Archaeology - infer evolutionary history of a network.
• VI-Cut - find a clustering that best matches imperfectly-known cluster hints.