FSA pipeline

FSA specifications

Information


Unique identifier OMICS_03735
Name FSA
Alternative name Fast Statistical Alignment
Interface Web user interface
Restrictions to use None
License GNU General Public License version 2.0
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Fast_statistical_alignment

Publication for Fast Statistical Alignment

library_books

Fast statistical alignment.

2009 PLoS Comput Biol
PMCID: 2684580
PMID: 19478997
DOI: 10.1371/journal.pcbi.1000392

FSA IN pipelines

 (3)
2014
PMCID: 4030478
PMID: 24915435
DOI: 10.1128/mBio.00894-14

[…] acceptable genes were concatenated end to end, producing a single continuous sequence for each isolate. concatenated sequences were then aligned against each other using fast statistical analysis (fsa), resulting in a multiple sequence alignment of the core genome (40). phylogenetic trees were estimated using raxml using 100 bootstraps and final trees drawn in figtree (41)., s.¬†epidermidis […]

2012
PMCID: 3463246
PMID: 23066504
DOI: 10.7554/eLife.00013.030

[…] distribution of morphogenic activity in the bacterial species tested (table 1), a sequence alignment of 16s rdna genes from each species was generated by iterative pairwise comparisons using fsa (bradley et al. 2009). poorly aligned regions were removed by gblocks version 0.91b (castresana 2000; talavera and castresana 2007) using default block parameters. a distance matrix (distance […]

2010
PMCID: 3224671
PMID: 21092133
DOI: 10.1186/1471-2148-10-360

[…] were retrieved, and we retrieved the rpob sequence from cellvibrio japonicus, a member of the family pseudomonadaceae, to serve as a putative outgroup. a multiple sequence alignment was built using fsa 1.14.5 [60], with default parameters and the '-nucprot' flag to align conceptual translations of the rpob genes, rather than the raw dna sequence, in order to preserve the correct reading frame […]

FSA institution(s)
Department of Mathematics, University of California Berkeley, Berkeley, CA, USA

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