Gblocks pipeline

Gblocks specifications

Information


Unique identifier OMICS_23397
Name Gblocks
Interface Web user interface
Restrictions to use None
Input data An alignment.
Input format FASTA
Computer skills Basic
Version 0.91
Stability Stable
Maintained Yes

Maintainer


  • person_outline Jose Castresana <>

Publication for Gblocks

Gblocks citations

 (70)
2018
PMCID: 5893858

[…] amino acid sequence of 412 conserved proteins of the 13 sequenced m. florum strains and m. capricolum was made with clustalo (v.1.2.1) (55). unaligned and low-confidence regions were removed with gblocks (v.0.91b) (56) to produce a sequence matrix of 138,476 amino acid sites. both phylogenetic trees (fig. 1b and c) were made from this alignment with seaview (v.4.6.1) (57). the distance tree […]

2018
PMCID: 5897751

[…] ncbi database. the retrieved sequences together with the corresponding query were aligned with muscle v3.7 (edgar, 2004) and informative alignment blocks were retained for further analysis using gblocks v0.91b (talavera and castresana, 2007). prottest v3.4 (abascal et al., 2005) was used for selecting the best evolutionary model according to the akaike information criterion values (aic), […]

2018
PMCID: 5848443

[…] the proteins in the two ortholog groups in which ehp swps were clustered were first aligned with the online mafft program using the l-ins-i iterative refinement setting and then trimmed with gblocks with less stringent settings (allowing smaller final blocks, gap positions in the final blocks and less strict flanking positions). a bayesian inference method was also used to infer […]

2018
PMCID: 5874628

[…] the isolates by using ezbiocloud [34]. the phylogenetic analysis was performed on the phylogeny online platform [35]. this software aligned the sequences with muscle (v3.8.31), curated them with gblocks (v0.91b), reconstructed the phylogenetic tree using the maximum likelihood method implemented in the phyml program (v3.1/3.0 alrt) and the tree rendering performed with treedyn (v198.3). 13 […]

2018
PMCID: 5812350

[…] alignments were removed using gblocks v.0.91b (castresana, 2000; talavera and castresana, 2007) with default parameters, except that all gap positions were allowed. all original alignments and the gblocks-edited versions were concatenated separately to generate supermatrices. four more supermatrices of original and gblocks-edited alignments for non-genic regions (igs + intron, hereafter: ngs) […]

Gblocks institution(s)
Department of Physiology and Molecular Biodiversity, Institute of Molecular Biology of Barcelona, CSIC, Barcelona, Spain
Gblocks funding source(s)
Supported by a research grant in bioinformatics from the Fundaci6n BBVA (Spain), and grant number BIO2002- 04426-C02-02 from the Plan Nacional de Investigacion Cientifica, Desarrollo e Innovacion Tecnologica (I+D+I) of the MEC, cofinanced with FEDER funds.

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