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.

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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:

• Pathogens genomics
  • MentaLiST, frugal and accurate Multi-Locus Sequence Typing. Paper.
  • PRINCE, calling Copy-Number Variants from NGS data. Paper.
  • HyAsP, a hybrid assembler for plasmids. Paper.
  • PathoGiST, clustering pathogen isolates by combining multiple genotyping signals. Paper.
• NGS tools
  • Freddie, long reads isoform discovery. Paper.
  • Genion,long reads gene fusion discovery, paper in preparation.
  • HASLR, hybrid long reads genome assembly. Paper.
  • CoLoRMap, hybrid long reads correction. Paper.
  • LRCstats, evaluating long reads correction tools. Paper.
  • Calib, clustering UMI-barcoded sequencing data. Paper.
• Comparative genomics
  • ANGeS, reconstructing ancestral genome maps. Paper.
  • SPP-DCJ, Small Parsimony for Natural Genomes in the DCJ-Indel Model. Paper.
  • SCJ-with-SGD, the Single-Cut-or-Join distance and median with duplicated genes. Paper.
  • PhySca, the Single-Cut-and-Join (SCJ) small parsimony problem for weighted gene adjacencies. Paper.
  • DeCoStar, reconstructing parsimonious histories of gene adjacencies. Paper.
  • DeClone, evolutionary scenarios for gene adjacencies in a Gibbs-Boltzmann framework. Paper.
  • ADseq, comparative scaffolding. Paper.
  • ecceTERA, gene tree species tree reconciliation. Paper.
  • MaxTiC, ranking nodes in a phylogeny using inferred horizontal gene transfers. Paper.
• Paleogenomics and ancient DNA
  • FPSAC, fast phylogenetic scaffolding of ancient contigs. Paper
  • AGapEs, comparative gap filling in ancient DNA assemblies. Paper.
  • EWRA, Edge-Weighted Reconstruction integrating aDNA Assembly graph. Paper.
• Other
  • flowLearn, a machine-learning algorithm for gating flow cytometry data. Paper
  • RNA-unchained, Chaining sequence/structure seeds for computing RNA similarity. Paper.
  • DLTCount, counting and sampling gene family histories. Paper.

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Older stuff.

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

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

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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, Supp. Mat..

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

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