Gblocks protocols

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 IN pipelines

 (225)
2018
PMCID: 5811012
PMID: 29438384
DOI: 10.1371/journal.pone.0192439

[…] retrieved from genbank or the marine microbial eukaryote transcriptome sequencing project (mmetsp) database. a segment of 1,677 positions on the 18s rrna gene was selected through a combination of gblocks [22] and manual editing to use for tree building using muscle [23]. approximate maximum likelihood trees were constructed using fasttree v2.1 [24] in ‘accurate mode’ (-mlacc 2-slowmmi) […]

2018
PMCID: 5811015
PMID: 29438445
DOI: 10.1371/journal.pone.0192723

[…] proteins with the sequence percent identity to the query higher than 35% were aligned using muscle v. 3.8.31 with default parameters [20]. poorly aligned regions of the alignment were removed using gblocks [21] with the following parameters: -b3 = 10; -b4 = 2; -b5 = h. maximum likelihood phylogenetic tree was inferred using the iqtree multicore v.1.5.3 with jtt + g4 model [22]. branch supports […]

2018
PMCID: 5813590
PMID: 29456885
DOI: 10.7717/peerj.4331

[…] had previously been reported as contaminants (lindgren et al., 2012)., sequences were aligned using mafft v7.158b (katoh et al., 2002) with default settings. the alignments were then processed with gblocks 0.91b (castresana, 2000) to eliminate poorly aligned positions from the final matrix. to increase the number of phylogenetically informative variable sites, gaps were allowed in up to half […]

2018
PMCID: 5813590
PMID: 29456885
DOI: 10.7717/peerj.4331

[…] to eliminate poorly aligned positions from the final matrix. to increase the number of phylogenetically informative variable sites, gaps were allowed in up to half of the genera, as determined by gblocks., preliminary rounds of phylogenetic inference using a maximum likelihood analysis in raxml v.8.2.4 (stamatakis, ludwig & meier, 2005) enabled us to identify and remove contaminants […]

2018
PMCID: 5824068
PMID: 29483968
DOI: 10.7150/jgen.22986

[…] genomes, including the 3 genomes sequenced in this study. a total of 1,355 conserved proteins were identified using orthofinder 15, aligned using t-coffee 16, concatenated and trimmed using gblocks 17 before the resulting alignment (296,082 amino acids in length) was used to construct a core genome maximum likelihood phylogeny using phyml-sms with sh-alrt branch support method 18. […]

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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