catfasta2phyml protocols

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catfasta2phyml specifications

Information


Unique identifier OMICS_23489
Name catfasta2phyml
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some FASTA alignments.
Input format FASTA
Output format PHYML
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.0
Stability Stable
Requirements
Getopt::Long, Pod::Usage
Maintained Yes

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  • person_outline Johan Nylander <>

catfasta2phyml in pipeline

2015
PMCID: 4777114
PMID: 26715088
DOI: 10.1534/g3.115.023432

[…] custom perl script. then, all sequences were aligned for each locus independently using mafft v7.050b (–auto option) (). the individual alignments were concatenated to a matrix with the perl script catfasta2phyml.pl (available at https://www.abc.se/~nylander/catfasta2phyml/). the matrix was filtered to eliminate divergent and ambiguously aligned regions with gblocks v 0.91b () (default […]


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catfasta2phyml in publications

 (3)
PMCID: 5680696
PMID: 29102123
DOI: 10.1016/j.vetmic.2017.09.016

[…] protein clusters were aligned with muscle (). amino acid alignments were then translated back into nucleotide sequences using the pal2nal (), concatenated and transformed into phyml format with catfasta2phyml/catfasta2phyml.pl script to use for raxml phylogenetic estimation under a gtr model and 100 bootstrap replicates (). get_homologues was also used for the pan genome analysis, using […]

PMCID: 5158034
PMID: 27977751
DOI: 10.1371/journal.pone.0168160

[…] locus fragments (adk, fumc, gyrb, icd, mdh, pura and reca) retrieved from the sequenced genomes. the corresponding genes of each strain were aligned with mafft v7.130b [], and concatenated using catfasta2phyml.pl script. further the maximum likelihood method based on the hasegawa-kishino-yano model implemented in the mega v.6 [] was used to create a phylogenetic tree. the core genome single […]

PMCID: 5114724
PMID: 27855631
DOI: 10.1186/s12862-016-0825-7

[…] paralogs stand out by being markedly divergent from genes in related species, while in trees paralogs end up in outgroup positions. the final alignments of the 47 proteins were concatenated using catfasta2phyml v1.0 (https://github.com/nylander/catfasta2phyml) yielding a total of 37,410 aligned amino acid positions. this alignment, shown in additional file , was used in its entirety […]


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