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MARE specifications

Information


Unique identifier OMICS_16336
Name MARE
Alternative name MAtrice REduction
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 0.1.2
Stability Stable
Maintained Yes

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MARE citations

 (5)
call_split

Multiple Lines of Evidence from Mitochondrial Genomes Resolve Phylogenetic Relationships of Parasitic Wasps in Braconidae

2016
Genome Biol Evol
PMCID: 5630901
PMID: 27503293
DOI: 10.1093/gbe/evw184
call_split See protocol

[…] stringent criterion that partitions with more than 10% negative pairwise similarity scores (44 out of 435 in our data with 30 taxa) were excluded in subsequent analyses. For the amino acid sequences, MARE (http://mare.zfmk.de, last accessed 8 Aug, 2016) (), based on weighted geometry quartet mapping (), was used to calculate the relative quality of information of each single gene within the matrix […]

library_books

Genome scale data suggest reclassifications in the Leisingera Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.

2014
Front Microbiol
PMCID: 4127530
PMID: 25157246
DOI: 10.3389/fmicb.2014.00416

[…] “core genes” only, i.e., those alignments containing sequences from all genomes, (ii) a “full” matrix using all alignments comprising at least four sequences, (iii) the same matrix but filtered with MARE (http://mare.zfmk.de) (Meusemann et al., ) without removing organisms. Additionally, two smaller matrices of preselected genes were analyzed, using the distinct sets of 31 genes, respectively, su […]

library_books

Transcriptome Data Reveal Syndermatan Relationships and Suggest the Evolution of Endoparasitism in Acanthocephala via an Epizoic Stage

2014
PLoS One
PMCID: 3919803
PMID: 24520404
DOI: 10.1371/journal.pone.0088618

[…] webpage (http://molevol.cmima.csic.es). Subsequent concatenation resulted in a supermatrix of 19 taxa and 1,180 genes. To find a subset of genes suitable for phylogenetic reconstructions, we applied MARE v0.1-rc (MAtrix REduction) . This tool uses quartet mapping with extended geometry mapping to assign information content to a protein sequence. Additionally, data availability is taken into accou […]

library_books

Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

2013
Mol Biol Evol
PMCID: 3879454
PMID: 24140757
DOI: 10.1093/molbev/mst196

[…] using TREE-PUZZLE v.5.2 (; http://www.tree-puzzle.de, last accessed November 4, 2013), applying the BLOSUM62 substitution matrix () as the BLOSUM62 substitution matrix is implemented in the software MARE (; http://mare.zfmk.de, last accessed November 4, 2013). Fig. 5.For each gene in the data set M_Ento, we calculated the proportions of quartets that predominantly supported either topology T1, T2 […]

call_split

Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data

2012
Genome Biol Evol
PMCID: 3542558
PMID: 23175716
DOI: 10.1093/gbe/evs104
call_split See protocol

[…] a, 1,579 genes, 744402 amino acid positions but shows only a density of 34.2%. Therefore, different approaches to reduce the amount of missing data were applied: 1) The first matrix was created using MARE (v0.1.2-rc) () (http://mare.zfmk.de) where genes and taxa are selected based on information content and data availability. Applying this approach the dictyopteran Hodotermopsis sjoestedti, Blatte […]

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