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|Alternative name||Fast Phylogenetic Scaffolding of Ancient Contigs|
|Interface||Command line interface|
|Restrictions to use||None|
No version available
- person_outline Cedric Chauve
Publication for Fast Phylogenetic Scaffolding of Ancient Contigs
Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes
[…] 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
[…] 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
[…] 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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