Computational Methods for Paleogenomics and Comparative Genomics

This page contains software developed in our group at Simon Fraser University, as well as links to software and websites developed in collaboration with other groups.
Github. The most recent versions of the software developed in our lab and with our collaborators are available from our GitHub repository. The main tools available there and on some of our collaborators github sites:
Older stuff.

FragAnchor. GPI-Anchored Protein Prediction.
Website: FragAnchor.
References: Paper.

Amniotes ancestral genome. reconstructing the gene order of the amniote ancestral genome/.
Code and data
Reference, Reconstructing the architecture of the ancestral amniote genome

splitMixed. Finding in a matched tumor/normal paired-end reads dataset a consistent explanation for a (mixed) tumor-subset of deletions.
Author: Roland Wittler.
References: Paper, Supp. Mat..

BRASERO. Benchmarking RNA Secondary Structure Comparison Algorithms.
Website: BRASERO.
Author: Julien Allali.
References, Poster, Paper.

Korak. Probabilistic exploration of the space of gene tree/species tree reconciliations.
Code and data.
Author: Jean-Philippe Doyon.
References: Paper.
References: Poster, Paper.