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Protocols

Gblocks specifications

Information


Unique identifier OMICS_23397
Name Gblocks
Alternative name gBlock
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

 (1855)
library_books

Components of a new gene family of ferroxidases involved in virulence are functionally specialized in fungal dimorphism

2018
Sci Rep
PMCID: 5955967
PMID: 29769603
DOI: 10.1038/s41598-018-26051-x

[…] the above mentioned genes could be obtained using the delta-delta CT (ΔΔCT) method normalizing for rRNA 18S. Multiple protein sequence alignment was conducted with MUSCLE program, and then curated by Gblocks to select conserved blocks of amino acids. Computational phylogenetic analysis was performed using PhyML software. Phylogenetic relationship was inferred by maximum likelihood-based statistica […]

library_books

Multiple origins of green blood in New Guinea lizards

2018
Sci Adv
PMCID: 5955620
PMID: 29774232
DOI: 10.1126/sciadv.aao5017

[…] screened for matches to the UCE probes, and nontargets and paralogs were removed in PHYLUCE. The resulting regions were aligned using MAFFT (), and quality-trimmed using a parallelized wrapper around Gblocks (). We created three data sets from our “all taxa” data set. First, to examine the effects of number of loci in phylogeny estimation, we removed 21 individuals with <1000 UCE loci to create a […]

library_books

Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast

2018
BMC Genomics
PMCID: 5952469
PMID: 29764372
DOI: 10.1186/s12864-018-4751-5

[…] ssing of the results with a custom script. Sequences from each resulting CDS cluster were aligned with MAFFT 7.215 with the “--auto” option and default parameters [], the alignment was optimized with Gblocks 0.91 using options “-b3=10 -b4=3 -b5=n” [] and used for the reconstruction of phylogeny with PhyML 3.1 [] if it was longer than 200 nucleotides and contained on average at least 15 nucleotide […]

library_books

The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites

2018
Sci Rep
PMCID: 5954100
PMID: 29765106
DOI: 10.1038/s41598-018-25981-w

[…] where MAFFT is used to build the protein alignment. Translation was done under the invertebrate mt genetic code. Additionally, poorly aligned sites were excluded using the alignment cleaning program GBlocks (implemented within TranslatorX) under the default parameters. Finally, the single alignments were concatenated into one data set, with a final length of 6,879 bp, using DAMBE 5.5.24.The datas […]

library_books

Mobilization of retrotransposons as a cause of chromosomal diversification and rapid speciation: the case for the Antarctic teleost genus Trematomus

2018
BMC Genomics
PMCID: 5941688
PMID: 29739320
DOI: 10.1186/s12864-018-4714-x

[…] tained 282 informative sites for DIRS1, 167 for Gypsy RT/RH, 153 for Gypsy INT and 220 for Copia.Multisequence alignments were performed with MAFFT v7 and ambiguously aligned sites were removed using Gblocks []. Neighbor-joining (NJ) phylogenies were obtained using MEGA 5.2.2 []. The best-fit model was selected with Topali v2, implemented using PhyML [] and the JTT model [] with gamma distribution […]

library_books

A phylogenetic analysis of the Primnoidae (Anthozoa: Octocorallia: Calcaxonia) with analyses of character evolution and a key to the genera and subgenera

2018
BMC Evol Biol
PMCID: 5930830
PMID: 29716521
DOI: 10.1186/s12862-018-1182-5

[…] 828 bp, COI: 675 bp, 28S:600bp, and 18S: 728 bp (Additional file ). Gblocks v0.91b [], utilized through the Phylogeny.fr sever [], was used to remove ambiguous regions of each 18S and 28S alignment. Gblocks options were set to allow less stringent flanking regions and gap positions, and the resulting parameters were - minimum number of sequences for a conserved position: 78; minimum number of seq […]

Citations

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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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