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MafFilter specifications


Unique identifier OMICS_06743
Name MafFilter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability No
Maintained No




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Publication for MafFilter

MafFilter citations


Fine Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots

PMCID: 5844332
PMID: 29263029
DOI: 10.1534/genetics.117.300502

[…] were projected against the two reference genomes of each species: ipo323 for z. tritici and sto4ir-1.1.1 for z. ardabiliae (; ). the projected alignments in maf format were filtered using the maffilter program () with the following filters: (1) each syntenic block was realigned using mafft (), and blocks with >10 kb were split for computational efficiency; (2) only blocks […]


Strong Selective Sweeps on the X Chromosome in the Human Chimpanzee Ancestor Explain Its Low Divergence

PLoS Genet
PMCID: 4537231
PMID: 26274919
DOI: 10.1371/journal.pgen.1005451

[…] orangutan and macaque from scally et al. [] was used as input. in order to remove badly sequenced and / or ambiguously alignment regions, we filtered the input 5-species alignments using the maffilter program []. we sequentially applied several filters to remove regions with low sequence quality score and high density of gaps. details on the filters used can be found in the supplementary […]


The de novo genome assembly and annotation of a female domestic dromedary of North African origin

Mol Ecol Resour
PMCID: 4973839
PMID: 26178449
DOI: 10.1111/1755-0998.12443

[…] genome assemblies using mugsy v1.2.3 (angiuoli & salzberg ) with a maximum distance of 500 bp for chaining anchors into locally collinear blocks. the final alignment blocks were filtered using maffilter v1.1.0 (dutheil et al. ) with the following criteria: using a sliding window of 10 bp, we excluded the window from the alignment if more than five gaps (including ‘n’) were present […]

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MafFilter institution(s)
Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany

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