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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

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

[…] contigs of a genome of interest with related assembled genomes has proven to be a useful approach to improve the assembly of fragmented genomes, especially bacterial genomes []. among such methods, fpsac [] was introduced to improve ancient genome assemblies within a phylogenetic context. it was applied to adna contigs from the y. pestis strain responsible for the medieval london bubonic plague […]


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

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

[…] 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 [], […]


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

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

[…] sequences are avalaible in additional file ., 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 […]

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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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