MafFilter protocols

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MafFilter specifications

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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 in pipeline

2017
PMCID: 5844332
PMID: 29263029
DOI: 10.1534/genetics.117.300502

[…] higher than the flanking regions. thus 2578 and 862 hotspots were identified in z. tritici and z. ardabiliae, respectively. the z. ardabiliae hotspots were mapped onto the z. tritici genome using maffilter’s liftover function (). we considered a hotspot in z. tritici as colocalizing with a hotspot in z. ardabiliae if the distance between them was <1 kb, and if no other hotspot was found […]


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MafFilter in publications

 (3)
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 […]

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 […]

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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