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Protocols

BMGE specifications

Information


Unique identifier OMICS_13030
Name BMGE
Alternative name Block Mapping and Gathering with Entropy
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data DNA sequences
Input format FASTA, PHYLIP
Output data Multiple sequence alignment
Output format PHYLIP, FASTA, NEXUS, HTML
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.12
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Alexis Criscuolo

Publication for Block Mapping and Gathering with Entropy

BMGE citations

 (126)
call_split

Trypanosomal mitochondrial intermediate peptidase does not behave as a classical mitochondrial processing peptidase

2018
PLoS One
PMCID: 5919513
PMID: 29698456
DOI: 10.1371/journal.pone.0196474
call_split See protocol

[…] ogs, 7 genes of closely related thimet peptidases, 9 genes of OpdA and 6 genes of Dcp () obtained by a BLAST search were aligned using Muscle 3.8.425 software (default parameters) [] and trimmed with BMGE 1.12 (-b 5 -m BLOSUM30) []. Protein evolution model was selected by ProtTest 3.2 [] to reconstruct phylogenetic tree by PhyML 3.1 (topology search: best of NNIs and SPRs, initial tree: BioNJ, Sub […]

library_books

HMMER Cut off Threshold Tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut off threshold

2018
PLoS One
PMCID: 5868777
PMID: 29579071
DOI: 10.1371/journal.pone.0193757

[…] i) mode for PGs and the multiple domain iteration (E-INS-i) mode for PLCs and subsequently corrected by Rascal []. PHYML3 [] using the LG model was used for phylogenetic tree reconstruction following BMGE [] trimming with BLOSUM62 matrix and an entropy cut-off of 0.9. Complete trees were constructed with all identified sequences. The training tree of the second PLC analysis is an excerpt of the PL […]

library_books

Cysteine peptidases of Eudiplozoon nipponicum: a broad repertoire of structurally assorted cathepsins L in contrast to the scarcity of cathepsins B in an invasive species of haematophagous monogenean of common carp

2018
PMCID: 5840727
PMID: 29510760
DOI: 10.1186/s13071-018-2666-2

[…] e CD-HIT software []. Divergent and incomplete sequences were manually removed, which resulted in a dataset of 288 sequences. These were aligned using the MAFFT [] and the alignment was trimmed using BMGE (239 sites) []. We inferred a maximum-likelihood tree using the best-fit model (LG + C60 + G), and tested the topology with 10,000 ultrafast bootstraps in IQ-TREE []. Bayesian inference of phylog […]

library_books

Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome

2018
Front Microbiol
PMCID: 5797428
PMID: 29434576
DOI: 10.3389/fmicb.2018.00028

[…] ained in a genome for a ribosomal protein, the best was selected. The sequences were extracted and each family was aligned using the MAFFT program (”linsi” algorithm) (). Alignments were curated with BMGE (version 1.12, default parameters and BLOSUM 45) () and then checked manually. In several cases, sequences identified as part of a given ribosomal protein family did not align well and were exclu […]

library_books

Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super Group

2018
Genome Biol Evol
PMCID: 5793813
PMID: 29360967
DOI: 10.1093/gbe/evy014

[…] eukaryotes were selected (see , online). Extensive efforts were made to exclude contamination and paralogs, as described in the supplementary text, online. Poorly aligned sites were excluded using BMGE (), resulting in an alignment of 97,002 amino acid (AA) sites with <25% missing data for both 61- and 64-taxon data sets (, online). […]

library_books

Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis

2018
eLife
PMCID: 5953543
PMID: 29697049
DOI: 10.7554/eLife.34292.028

[…] ilable at on dryad at DOI: https://doi.org/10.5061/dryad.qp745/4.For the RquA analyses, sequences were aligned using MAFFT-linsi version 7.273 () and regions of ambiguous alignment were removed using BMGE 1.12 () with default settings. Evolutionary model selection for maximum-likelihood analysis was performed on all C-series mixture models (C10-C60) with the LG exchangeability matrix, with and wit […]

Citations

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BMGE institution(s)
Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Paris, France
BMGE funding source(s)
PhyloCyano project of the Agence Nationale de la Recherche (ANR; 07-JCJC-0094-01)

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