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Table 1 Available filters

From: MafFilter: a highly flexible and extensible multiple genome alignment files processor

Filter name

MafIterator class

Characteristics

Data extraction

Subset

SequenceFilterMafIterator

Extract alignments for a given set of species, filter duplicates.

Merge

BlockMergerMafIterator

Merge consecutive blocks if they are syntenic.

Concatenate

ConcatenateMafIterator

Concatenate consecutive blocks up to a given length, regardless of coordinates.

XFullGap

FullGapFilterMafIterator

Remove gap positions for a given ingroup.

FeatureFilter

FeatureFilterMafIterator

Remove regions from a given feature file.

ExtractFeature

FeatureExtractor

Remove regions outside the ones specified in a given feature file.

SelectChr

ChromosomeMafIterator

Extract alignments from a given chromosome.

Block filtering

MinBlockLength

BlockLengthMafIterator

Remove alignment blocks with too little sites.

MinBlockSize

BlockSizeMafIterator

Remove alignment blocks with too little sequences.

Sliding window-based alignment processing

AlnFilter

AlignmentFilterMafIterator

}Remove ambiguously aligned regions.

AlnFilter2

AlignmentFilterMafIterator2

 

EntropyFilter

EntropyFilterMafIterator

Remove highly variable regions.

MaskFilter

MaskFilterMafIterator

Remove masked regions.

QualityFilter

QualityFilterMafIterator

Remove regions with low quality.

Statistical analysis

WindowSplit

WindowSplitMafIterator

Split blocks into windows of given size.

SequenceStatistics

SequenceStatisticsMafIterator

Compute a user-defined selection of statistics, such as character frequencies, alignment size and length, frequency spectrum, counts of fixed vs. polymorphic sites and pairwise divergences. Results are output to a CSV file together with block coordinates for subsequent analysis.

DistanceEstimation

(several classes) a

Estimate distance matrix between species.

DistanceBased-Phylogeny

DistanceBasedPhylogenyReconstructionMafIterator

Reconstruct block-wise phylogenies using distance-based methods (W/UPGMA, Neighbor joining, BioNJ)

NewOutgroup

NewOutgroupMafIterator

Reroot a block-wise phylogenetic tree according to a given species.

DropSpecies

DropSpeciesMafIterator

Remove leaves from block-wise trees for agiven species.

Output

Output

OutputMafIterator

Write blocks to a file in MAF format.

OutputAlignments

OutputAlignmentMafIterator

Write blocks into an alignment file, forinstance Fasta or Clustal, using Ensemblsyntax for storing coordinates.

OutputTrees

OutputTreeMafIterator

Write associated trees to a Newick file.

VcfOutput

VcfOutputMafIterator

Call SNPs for each block and write them in a VCF file [17].

  1. adepending on the method used.