From: MafFilter: a highly flexible and extensible multiple genome alignment files processor
Statistic name | MafStatistic class | Characteristics |
---|---|---|
Block structure | ||
BlockLength | BlockLengthMafStatistics | Report the alignment length of each block. |
SequenceLength | SequenceLengthMafStatistics | Report the number of nucleotides of a given species in each block. |
BlockSize | BlockLengthMafStatistics | Report the number of sequences in each block. |
AlnScore | AlignmentScoreMafStatistics | Report the alignment score for each block, if any. |
Block content | ||
BlockCounts | CharacterCountsMafStatistics | Compute the frequency of each character in each block. |
SiteStatistics | SiteMafStatistics | Compute site-base statistics: number of sites without gap, number of complete sites (no gap, no unresolved character), number of parsimony-informative sites in each block. |
Population genetics | ||
PairwiseDivergence | PairwiseDivergenceMafStatistics | Compute the sequence dissimilarity between two individuals. |
PolymorphismStatistics | PolymorphismMafStatistics | Compare two groups of sequences, and compute the number of fixed/polymorphic sites between and within each group. |
DiversityStatistics | SequenceDiversityMafStatistics | For a given group of sequences, compute the number of seggregating sites and Watterson’s theta. |
SiteFrequencySpectrum | SiteFrequencySpectrumMafStatistics | Compute the (unfolded) frequency spectrum for a given group of sequences. |
CountClusters | CountClustersMafStatistics | Compute the number of haplotype groups, given a certain mutation threshold, providing a tree has been previously computed. |