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]. |