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.