FASconCAT pipeline

FASconCAT specifications

Information


Unique identifier OMICS_16337
Name FASconCAT
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A nucleotide, amino acid and structure sequence fragments of same taxa to one super matrix.
Input format PHYLIP, CLUSTAL, FASTA
Output format FASTA, PHYLIP, NEXUS, XLS
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

Download


Versioning


Add your version

Maintainer


  • person_outline Patrick Kuck <>

FASconCAT IN pipelines

 (13)
2018
PMCID: 5846723
PMID: 29529094
DOI: 10.1371/journal.pone.0192502

[…] start and stop codons were trimmed and each locus was filtered using the phylogeny.fr gblocks [82] webpage using the least stringent settings; the six trimmed, filtered loci were concatenated with fasconcat [83] (tables 1, s2 table). the final 118-taxon alignment contained 103 phytophthora taxa, thirteen downy mildew taxa and two pythium s.l. outgroups; the 135-taxon alignment contained thirty […]

2018
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] protein sequences that were longer than 50 amino acids (1,241 of the 1,280 homologues) were selected using a python script (“filter_len.py”; available from github) and then concatenated using fasconcat-g v1.02 (113). data corresponding to appropriate substitutional models, the best partition scheme, phylogenomic tree reconstruction, and ultrafast bootstrap analyses were all inferred […]

2017
PMCID: 5381553
PMID: 28201585
DOI: 10.1093/gbe/evx022

[…] obtained in guidance v2.0 (sela et al. 2015) anchored by codons using mafft v7.0 (katoh and standley 2013) with 100 pseudoreplicate guide trees. concatenation of the multiple alignment was done by fasconcat (kück and meusemann 2010). manual curation was then performed in aliview (larsson 2014), and whenever local regions were misaligned we used the software “realign selected block” option […]

2017
PMCID: 5469757
PMID: 28611446
DOI: 10.1038/s41598-017-03445-x

[…] sp. (p. falciparum and p. vivax) and toxoplasma gondii was aligned using mafft v7114. highly variable sites were trimmed using trimal115. a supermatrix of the alignments was concatenated using fasconcat116. based on this alignment a maximum likelihood phylogenetic tree was constructed using raxml117, 118 based on amino acid input, gamma model, lg substitution matrix and 100 initial […]

2017
PMCID: 5487361
PMID: 28655915
DOI: 10.1038/s41598-017-04094-w

[…] correction. the selected genes were then trimmed using the defalut setting in gblocks49 to remove ambiguously aligned regions. genes were then concatenated into final supermatrix datasets using fasconcat50 for downstream phylogenetic analysis. phylogenetic relationships of ampharetids were infered using maximum likelihood (ml) in raxml51. prior to ml analyses, partitionfinderv1.1.152 […]

FASconCAT reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review FASconCAT