FASconCAT specifications

Information


Unique identifier OMICS_16337
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 citations

 (3)
2018
PMCID: 5846723

[…] 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 […]

2017
PMCID: 5557424

[…] strains previously characterized by weinert et al. [3]. the sequences of each locus were aligned with mafft version 7.271 [28] using the ‘l-ins-i’ algorithm and concatenated to a supermatrix using fasconcat version 1.0 [29]. the final dataset consisted of 100 rickettsia strains (32 from lacewings) and 3729 nucleotide positions in total. iq-tree version 1.5.3 [30] was then employed to 1) […]

2011
PMCID: 3123331

[…] sections (28s rrna: 725 base positions (bp); 18s rrna: 14 bp) were excluded with alicut [34]. in the ef1af2 alignment, no randomised positions were detected. single genes were concatenated using fasconcat version 1.0 [35]. the concatenated supermatrix of the masked approach included 4,315 characters while the unmasked supermatrix comprised 5,054 characters. all alignments (fasta format) […]

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