Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.

By Gerard Talavera, J. Castresana. Systematic Biology, 2007

5,291 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/763d42f71dd62eae18a63d1f85750cd14b2983b8

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Citations in the corpus

EDGAR: A software framework for the comparative analysis of prokaryotic genomes (2009, methodology): “Non matching parts of the alignments are masked using GBLOCKS [30] and then removed.”
Evolution of Oviposition Techniques in Stick and Leaf Insects (Phasmatodea) (2018, positive): “Multiple ambiguously aligned expansion regions were removed from the 28S alignment using GBlocks (Talavera and Castresana, 2007) with options for a “less stringent selection.”
An alignment confidence score capturing robustness to guide tree uncertainty. (2010, methodology): “To compare the performance of Gblocks and our method, we ran Gblocks on the simulation benchmark using two sets of parameters, ‘‘stringent’’ and ‘‘relaxed,’’ as deﬁned in Talavera and Castresana (2007).”
The impact of rRNA secondary structure consideration in alignment and tree reconstruction: simulated data and a case study on the phylogeny of hexapods. (2010, background): “Several studies in the past recommend the exclusion or masking of ambiguous positions to reduce the amount of potential noisy signal (Brinkmann and Philippe 1999; Hirt et al. 1999; Ruiz-Trillo et al. 1999; Talavera and Castresana 2007; Misof B and Misof K 2009).”
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations (2010, background): “Evolutionary comparisons of primary sequence data rely on the generation of a multiple sequence alignment that maximizes the likelihood of positional homology between nucleotides or amino acids by introducing gaps (1).”
Enriching the ant tree of life: enhanced UCE bait set for genome‐scale phylogenetics of ants and other Hymenoptera (2017, positive): “91b (Castresana 2000; Talavera & Castresana 2007), which we ran with reduced stringency settings of 0 5, 0 5, 12 and 7 for the b1–4 settings, respectively.”
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm (2014, methodology): “The alignments were refined using Gblocks [33] and loaded into MEGA5 [34] to construct the maximum-likelihood tree using default settings (Tamura-Nei model, uniform rates, and complete deletion) with 1,000 bootstraps.”
New World Bats Harbor Diverse Influenza A Viruses (2013, methodology): “Because of the highly divergent nature of the HA and NAL segments, all ambiguously aligned sites in these segments were removed using the Gblocks program [33].”
Structural Insight into How Bacteria Prevent Interference between Multiple Divergent Type IV Secretion Systems (2015, methodology): “Protein alignments were also trimmed of less-conserved regions using Gblocks (66), with these masked alignments also concatenated into a single data set (masked data set; 818 characters).”
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments (2010, methodology): “However, when considering dis-tantly-related sequences (e.g. level of divergence ×3), the ML approach (as well as the BioNJ and MP ones) needs a preliminary trimming step to infer significantly accurate trees, in agreement with results from previous simulation-based studies (e.g. [ 8]).”
Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life (2016, methodology): “Ambiguously aligned regions were removed from the final alignments using GBLOCKS (Castresana, 2000; Talavera & Castresana, 2007) with default settings, except that only sites where more than half of the sequences had gaps (‘halfgap’ option) were removed.”
Developments in the taxonomy of silica-scaled chrysophytes - from morphological and ultrastructural to molecular approaches (2013, neutral): “0.91b (Talavera and Castresana 2007).”
ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference (2020, background): “Gblocks Gblocks Remove sites that are gap rich and highly variable default [1]”
Resurrection and emendation of the Hypoxylaceae, recognised from a multigene phylogeny of the Xylariales (2017, methodology): “…processed via the Castresana Lab Gblocks Server at low stringency settings (allowing smaller final blocks and gap positions within the final blocks; see Talavera and Castresana 2007; Castresana 2000) and the multigene alignment (MGA) was created by concatenation of all genetic markers in Geneious.”