Table 1.

Available filters

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].

^a depending on the method used.