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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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Versioning


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Documentation


Maintainer


  • person_outline Johan Nylander

catfasta2phyml citations

 (6)
library_books

HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees

2018
Evol Bioinform Online
PMCID: 5768271
PMID: 29348708
DOI: 10.1177/1176934317742613

[…] tas.py”; if an exon is missing for a particular accession, Ns are added. Also with HybPhyloMaker4a, exons are aligned using MAFFT, and exons from the same gene are concatenated using the Perl script “catfasta2phyml.pl”. Optionally, exon and gene alignments can be adjusted to correct the reading frame with HybPhyloMaker4b. This option later allows not only for per-exon but also for per-codon partit […]

library_books

Convergence of plasmid architectures drives emergence of multi drug resistance in a clonally diverse Escherichia coli population from a veterinary clinical care setting

2017
PMCID: 5680696
PMID: 29102123
DOI: 10.1016/j.vetmic.2017.09.016

[…] thms. 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 the […]

library_books

Characterisation of Commensal Escherichia coli Isolated from Apparently Healthy Cattle and Their Attendants in Tanzania

2016
PLoS One
PMCID: 5158034
PMID: 27977751
DOI: 10.1371/journal.pone.0168160

[…] ping 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 n […]

call_split

A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group

2016
BMC Evol Biol
PMCID: 5114724
PMID: 27855631
DOI: 10.1186/s12862-016-0825-7
call_split See protocol

[…] ts, 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 for phylog […]

library_books

Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome Scale Methods: The Bacillus pumilus Group Case

2016
PLoS One
PMCID: 5033322
PMID: 27658251
DOI: 10.1371/journal.pone.0163098

[…] under study () and an E-value of 1E-30. Orthologous genes present in all microorganisms (BLAST defined core genes) were individually aligned using ClustalW2 [], and concatenated using the Perl script catfasta2phyml.pl (http://www.abc.se/~nylander/catfasta2phyml/). The alignment was trimmed using GBlock 0.91b [] and used to infer the evolutionary history of the strains with the Randomized Axelerate […]

library_books

Exploring a Nonmodel Teleost Genome Through RAD Sequencing—Linkage Mapping in Common Pandora, Pagellus erythrinus and Comparative Genomic Analysis

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

[…] a 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 parameter […]

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