Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.

By J. Castresana. Molecular biology and evolution, 2000

10,165 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/b3d4c8c107a815b4a754cf07aafae8872a2aec77

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Citations in the corpus

Identifying conserved genomic elements and designing universal bait sets to enrich them (2017, methodology): “…steps (phyluce_assembly_match_contigs_to_probes; min_coverage 80, min_identity 80), exported non-duplicate conserved loci to FASTA format, aligned the FASTA data usingmafft (Katoh & Standley 2013) and trimmed the resulting alignments using gblocks (Castresana 2000; Talavera & Castresana 2007).”
Complete nucleotide sequence and organization of the mitogenome of endangered Eumenis autonoe (Lepidoptera: Nymphalidae) (2010, methodology): “The well-aligned blocks from the amino acid and nucleotide sequences were selected with GBlocks 0.91b (Castresana, 2000) with the maximum number of contiguous non-conserved positions set to eight.”
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough (2011, background): “Despite the great progress in software development [19–22,52–54], our nine years of experience with large-scale multigene analyses [55] leads us to conclude that computer-assisted manual expertise is not yet dispensable.”
Phylogeny of the Infraorder Caridea Based on Mitochondrial and Nuclear Genes (Crustacea: Decapoda) (2009, methodology): “91b (Castresana 2000) to omit poorly aligned positions (GBlocks parameters optimized for dataset and modeled after previous studies (Porter et al.”
A dated molecular phylogeny for the Chironomidae (Diptera) (2012, methodology): “3) The postulated origin of the stem Chironomidae in the Permian is earlier than, but within, the posterior probability of the 269 (308–231) Ma estimate of Cranston et al. (2010), and deviates significantly from the mid Triassic date estimated by Bertone et al.”
Diversity of rock varnish bacterial communities from Black Canyon, New Mexico (2010, neutral): “91 [Castresana, 2000; Talavera and Castresana, 2007].”
A simple, fast, and accurate method of phylogenomic inference (2008, background): “However, trees constructed using GBLOCKS-treated alignments have been found to have dramatically weaker support, possibly because of excessive removal of informative sites by the program [17].”
Phylogenetics of Hydroidolina (Hydrozoa: Cnidaria) (2008, background): “91b (Castresana, 2000) with default parameters except the minimum length block was set to 5 and half the taxa were allowed to be gaps for any given position (Table 2).”
Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach (2005, methodology): “Highly variable regions of the multiple alignment were removed, and conserved regions were selected with Gblocks,”
TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees (2018, methodology): “One common method of data filtering is alignment masking [12, 13], despite some criticism [11].”
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi (2014, methodology): “Gblocks (80) was run with the options t = p and −b4 = 5 to remove poorly aligned regions, resulting in 38,423 positions.”
Around the world in 10 million years: biogeography of the nearly cosmopolitan true toads (Anura: Bufonidae) (2007, methodology): “Regions of the mtDNA that remained unalignable were deleted from analyses using default parameters in the program Gblocks version 0.91b ( Castresana, 2000 ) on the Gblocks server (http:// molevol.ibmb.csic.es/Gblocks.html).”
Phylogeny of the gastropod superfamily Cerithioidea using morphology and molecules (2011, methodology): “(2009) Cerithiidae Keen (1971); Houbrick (1978, 1992, 1993a, b); Spencer, Marshall & Willan (2009); CLEMAM (2010); IPMD (2006); Malacolog (Rosenberg, 2009) Bittiinae 71 Cerithiinae 114 Dialidae 8 Ponder & de Keyzer (1992) Diastomatidae 1 Houbrick (1981b) Litiopidae 16–18 Keen (1971); W.”