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:

• Plasmids bioinformatcs
  • PlasBin-flow, optimization-based binning of plasmid contigs from assembly graphs.
  • plASgraph2, detection of plasmid contigs in assembly graphs.
  • PlasEval, evaluating plasmids binning methods.
  • HyAsP, hybrid binning of plasmid contigs from assembly graphs.
• Pathogens genomics
  • MentaLiST, whole-genome and core-genome multi-locus sequence typing (MLST).
  • PRINCE, estimatig the copy number of VNTR.
  • PathoGiST, clustering pathogen isolates by combining multiple genotyping signals.
• NGS tools
  • TKSM, highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator.
  • Freddie, annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-reads.
  • Genion, detecting gene fusions from transcriptomics long reads.
  • HASLR, fast hybrid assembly of long reads.
  • CoLoRMap, hybrid correction of long reads.
  • LRCstats, evaluating long-reads error-correction methods.
  • Calib, alignment-free clustering of UMI tagged DNA molecules.
• Comparative genomics
  • AGO, a pipeline for ancestral gene orders reconstruction.
  • ANGeS, reconstructio of ancestral genomes maps.
  • SPP-DCJ, the small parsimony problem with the Single-Cut-or-Join distance.
  • SCJ-with-SGD, the directed Single-Cut-or-Join distance with duplicated genes.
  • PhySca, Single-Cut-or-Join small-parsimony for weighted gene adjacncies.
  • DeCoStar, reconstructing the ancestral organization of genes or genomes using reconciled phylogenies .
  • DeClone, Eovlution of genes neighborhood within reconciled phylogenies: an ensemble approach.
  • ADseq, joint scaffolding extant and ancestral genomes.
  • ecceTERA, gene tre/species tree reconcliation.
  • MaxTiC, ranking of a phylogenetic tree by maximum time consistency with lateral gene transfers.
• Paleogenomics and ancient DNA
  • FPSAC, fast phylogenetic scaffolding of ancient contigs.
  • AGapEs, comparative scaffolding and gap filling of ancient bacterial genomes.
  • EWRA, joint scaffolding of ancient cotigs and ancestral genome reconstruction.
• Other
  • CEDAR, atools for manipluating a vector representation for phylogenetic trees.
  • flowGraph, automated identification of maximal differential cell populations in flow cytometry data.
  • flowLearn, a machine-learning tool for gating flow cytometry data.
  • RNA-unchained, Chaining sequence/structure seeds for computing RNA similarity.
  • DLTCount, counting and sampling gene family histories.

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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.