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. The most recent versions of the software developed in our lab and with our collaborators are available from our GitHub repository. Previous versions of selected software, specific data sets and software available through websites are provided below.


FPSAC: Fast Phylogentic Scaffolding of Ancient Contigs, applied to the Black Death data set.
Code, data.
Authors: Ashok Rajaraman, Eric Tannier, Cedric Chauve.


ANGES: reconstructing ANcestral GEnomeS maps. Computing Contiguous Ancestral Regions from the comparision of related extant genomes.
Code, data, references.
Authors: Bradley Jones, Ashok Rajaraman, Eric Tannier, Cedric Chauve.


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


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


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.


RNA StrAT. RNA Structure Analysis Toolkit
Website: RNA StrAT
Author: Valentin Guignon.
References: Poster.