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Table 2 Available statistics

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.