FASconCAT protocols

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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

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Maintainer


  • person_outline Patrick Kuck <>

FASconCAT in pipelines

 (14)
2018
PMCID: 5885362
PMID: 29618317
DOI: 10.1186/s12864-018-4615-z

[…] orthologs present in all species were extracted using custom bash scripts and aligned using muscle 3.8.31 []. we subsequently trimmed the alignment using trimal [] and generated a super matrix with fasconcat []. we used raxml [] to generate a maximum likelihood tree using the jtt + i + g + f model of evolution and 1000 bootstraps., we aligned the pe sequence reads back to the draft prairie […]

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 (). data corresponding to appropriate substitutional models, the best partition scheme, phylogenomic tree reconstruction, and ultrafast bootstrap analyses were all inferred […]

2017
PMCID: 5347184
PMID: 28293680
DOI: 10.1128/mSystems.00001-17

[…] were first aligned at the amino acid level using clustalw version 2.0 () and then back-translated to dna sequences using pal2nal (). the alignment of all orthologous sequences was concatenated using fasconcat (). the gene tree was constructed using phyml ()., accession numbers for chromosomes and plasmids are listed in ., this work was supported by a grant from the danish directorate for food, […]

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

[…] core-coding dna gene alignments were obtained in guidance v2.0 () anchored by codons using mafft v7.0 () with 100 pseudoreplicate guide trees. concatenation of the multiple alignment was done by fasconcat (). manual curation was then performed in aliview (), and whenever local regions were misaligned we used the software “realign selected block” option and updated the information […]

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

[…] plasmodium sp. (p. falciparum and p. vivax) and toxoplasma gondii was aligned using mafft v7. highly variable sites were trimmed using trimal. a supermatrix of the alignments was concatenated using fasconcat. based on this alignment a maximum likelihood phylogenetic tree was constructed using raxml, based on amino acid input, gamma model, lg substitution matrix and 100 initial bootstrap […]


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FASconCAT in publications

 (53)
PMCID: 5930637
PMID: 29743928
DOI: 10.1186/s12983-018-0262-0

[…] regions were manually removed and the exons were concatenated for each gene alignment. all sequences were trimmed to contain only complete codons triplets and alignments were concatenated using fasconcat-g 1.02 (https://www.zfmk.de/en/research/research-centres-and-groups/fasconcat) to produce a super-matrix consisting of 10,999 aligned positions. the partition scheme and selected models […]

PMCID: 5885362
PMID: 29618317
DOI: 10.1186/s12864-018-4615-z

[…] orthologs present in all species were extracted using custom bash scripts and aligned using muscle 3.8.31 []. we subsequently trimmed the alignment using trimal [] and generated a super matrix with fasconcat []. we used raxml [] to generate a maximum likelihood tree using the jtt + i + g + f model of evolution and 1000 bootstraps., we aligned the pe sequence reads back to the draft prairie […]

PMCID: 5906903
PMID: 29617768
DOI: 10.1093/gigascience/giy034

[…] orthologue in an orthogroup, the longest was selected. the remaining 897 orthogroups were re-aligned using mafft v7.267, trimmed with noisy v1.5.12, and concatenated into a supermatrix using fasconcat v.1.0 []. a supermatrix ml tree was generated using raxml with the rapid hill climbing algorithm (default), with a protgammagtr amino acid substitution model and 100 bootstrap replicates. […]

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 [] webpage using the least stringent settings; the six trimmed, filtered loci were concatenated with fasconcat [] (tables , ). 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 downy […]

PMCID: 5809470
PMID: 29472910
DOI: 10.3389/fmicb.2018.00161

[…] genes were first aligned at the amino acid level using clustal w version 2.0 (), then back-translated to dna sequences using pal2nal (). the alignment of all orthologous genes was concatenated using fasconcat (). a gene tree was constructed using phyml ()., filtered reads were aligned against virulence-related genes described for the pandemic strain of v. parahaemolyticus rimd2210633; the chosen […]


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