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FPSAC specifications


Unique identifier OMICS_00041
Alternative name Fast Phylogenetic Scaffolding of Ancient Contigs
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Cedric Chauve

Publication for Fast Phylogenetic Scaffolding of Ancient Contigs

FPSAC citations


Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes

Microb Genom
PMCID: 5643016
PMID: 29114402
DOI: 10.1099/mgen.0.000123

[…] ion (from thousands of contigs to a handful of CARs) and a very small fraction of the final assembly that is not supported by aDNA reads.Applied to the same data set for the London strain, the method FPSAC [] was able to obtain a single scaffold based on parsimonious optimization. Comparing our resulting assembly to this single scaffold, we could identify two breakpoints between both assemblies; h […]


Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction

BMC Bioinformatics
PMCID: 5123302
PMID: 28185565
DOI: 10.1186/s12859-016-1262-8

[…] MULTIRES for 82 parameter combinations, varying segment lengths and window lengths from 15 to 85 at intervals of 10. We assessed our results by comparing against FPMAG. FPMAG is a method derived from FPSAC [], a tool for scaffolding ancestral bacterial contigs. While FPSAC and FPMAG are not intended for use on mammalian genomes, they use the maximum matching routine described in [], and the concep […]


Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence

BMC Genomics
PMCID: 4603589
PMID: 26450112
DOI: 10.1186/1471-2164-16-S10-S9

[…] Using Megablast [] we aligned the 2134 ancient Yersinia pestis contigs obtained by Bos et al.[] (avalaible at http://paleogenomics.irmacs.sfu.ca/FPSAC/, last accessed 19 june 2015) against the obtained ancestral genome, including chromosome and plasmids.We examine 2179 hits of length >102.5bp from 2087 contigs (see Additional file for the bim […]


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FPSAC institution(s)
Department of Mathematics, Simon Fraser University, Burnaby (BC), Canada; International Graduate Training Center in Mathematical Biology, Pacific Institute for the Mathematical Sciences, Vancouver (BC), Canada; INRIA Grenoble Rhône-Alpes, Montbonnot, France; Université de Lyon 1, Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR5558 Villeurbanne, France; LaBRI, Université Bordeaux I, Talence, France
FPSAC funding source(s)
Natural Sciences and Engineering Research Council of Canada Discovery Grant, a Pacific Institute for the Mathematical Sciences International Graduate Training Centre Fellowship and Agence Nationale pour la Recherche-10-BINF-01-01 Ancestrome

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