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Protocols

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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  • person_outline Patrick Kuck

FASconCAT citations

 (57)
call_split

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

2018
MBio
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18
call_split See protocol

[…] 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 […]

library_books

Genome sequencing of Rhinorhipus Lawrence exposes an early branch of the Coleoptera

2018
Front Zool
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 […]

library_books

New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus)

2018
BMC Genomics
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 […]

library_books

Improving the annotation of the Heterorhabditis bacteriophora genome

2018
GigaScience
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. […]

library_books

Multiple origins of downy mildews and mito nuclear discordance within the paraphyletic genus Phytophthora

2018
PLoS One
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 […]

library_books

Exploring the Genomic Traits of Non toxigenic Vibrio parahaemolyticus Strains Isolated in Southern Chile

2018
Front Microbiol
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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