Parallelization of the MAFFT multiple sequence alignment program

Katoh, Kazutaka; Toh, Hiroyuki

doi:10.1093/bioinformatics/btq224

Cited by 777 publications

(573 citation statements)

References 17 publications

Supporting

Mentioning

539

Contrasting

Unclassified

Order By: Relevance

“…Nucleotide sequences were translated into amino acids, imported into the CIPRES Science Gateway 45 and aligned using the E-INS-i search strategy in MAFFT 46 . Alignments were converted into relaxed phylip format.…”

Section: Identification and Phylogenetic Analysis Of Nbs-lrr Genesmentioning

confidence: 99%

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

et al. 2013

View full text Add to dashboard Cite

Section: Identification and Phylogenetic Analysis Of Nbs-lrr Genesmentioning

confidence: 99%

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

et al. 2013

View full text Add to dashboard Cite

“…Subsequently, each ''raw'' gene dataset was aligned using MAFFT v7.045b (Katoh et al, 2002;Katoh and Toh, 2010) and the ambiguously aligned positions were masked with the Block Mapping and Gathering with Entropy (BMGE v1.1) software (parameters: -g 0.3 -b 5 -m BLOSUM62) (Criscuolo and Gribaldo, 2010). Single gene trees were constructed with FastTree (Price et al, 2009) and each tree was examined by eye to identify and remove paralogues and contaminants.…”

Section: Basic Phylogenomic Dataset Constructionmentioning

confidence: 99%

Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages

Gentekaki

Kolísko

Boscaro

et al. 2014

Molecular Phylogenetics and Evolution

View full text Add to dashboard Cite

“…A BLAST search was performed to find related sequences of other dinoflagellates in GenBank. A SSU-LSU rDNA alignment was constructed using Mafft v6.952 based on the G-INS-I model with default parameters (Katoh and Toh, 2010). The alignment was manually edited.…”

Section: Alignment and Phylogenetic Analysesmentioning

confidence: 99%

Recent radiation in a marine and freshwater dinoflagellate species flock

et al. 2015

View full text Add to dashboard Cite

Processes of rapid radiation among unicellular eukaryotes are much less studied than among multicellular organisms. We have investigated a lineage of cold-water microeukaryotes (protists) that appear to have diverged recently. This lineage stands in stark contrast to known examples of phylogenetically closely related protists, in which genetic difference is typically larger than morphological differences. We found that the group not only consists of the marine-brackish dinoflagellate species Scrippsiella hangoei and the freshwater species Peridinium aciculiferum as discovered previously but also of a whole species flock. The additional species include Peridinium euryceps and Peridinium baicalense, which are restricted to a few lakes, in particular to the ancient Lake Baikal, Russia, and freshwater S. hangoei from Lake Baikal. These species are characterized by relatively large conspicuous morphological differences, which have given rise to the different species descriptions. However, our scanning electron microscopic studies indicate that they belong to a single genus according to traditional morphological characterization of dinoflagellates (thecal plate patterns). Moreover, we found that they have identical SSU (small subunit) rDNA fragments and distinct but very small differences in the DNA markers LSU (large subunit) rDNA, ITS2 (internal transcribed spacer 2) and COB (cytochrome b) gene, which are used to delineate dinoflagellates species. As some of the species co-occur, and all four have small but species-specific sequence differences, we suggest that these taxa are not a case of phenotypic plasticity but originated via recent adaptive radiation. We propose that this is the first clear example among free-living microeukaryotes of recent rapid diversification into several species followed by dispersion to environments with different ecological conditions.

show abstract

Parallelization of the MAFFT multiple sequence alignment program

Cited by 777 publications

References 17 publications

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages

Recent radiation in a marine and freshwater dinoflagellate species flock

Contact Info

Product

Resources

About