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FPSAC specifications

Information


Unique identifier OMICS_00041
Name FPSAC
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

Versioning


No version available

Maintainer


  • person_outline Cedric Chauve

Publication for Fast Phylogenetic Scaffolding of Ancient Contigs

FPSAC citations

 (3)
library_books

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

2017
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 […]

library_books

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

2016
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 […]

library_books

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

2015
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 […]

Citations

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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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