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class | bpp::MafStatisticsResult |
| General interface for storing statistical results. More...
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class | bpp::SimpleMafStatisticsResult |
| A simple maf statistics result, with only one value. More...
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class | bpp::MafStatistics |
| General interface for computing statistics based on a Maf block. More...
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class | bpp::AbstractMafStatistics |
| Partial implementation of MafStatistics, for convenience. More...
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class | bpp::AbstractMafStatisticsSimple |
| Partial implementation of MafStatistics, for convenience. More...
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class | bpp::PairwiseDivergenceMafStatistics |
| Computes the pairwise divergence for a pair of sequences in a maf block. More...
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class | bpp::BlockSizeMafStatistics |
| Computes the number of sequences in a maf block. More...
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class | bpp::BlockLengthMafStatistics |
| Computes the number of columns in a maf block. More...
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class | bpp::SequenceLengthMafStatistics |
| Retrieve the sequence length (number of nucleotides) for a given species in a maf block. More...
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class | bpp::AlignmentScoreMafStatistics |
| Retrieves the alignment score of a maf block. More...
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class | bpp::AbstractSpeciesSelectionMafStatistics |
| Partial implementation of MafStatistics for method working on a subset of species, in a site-wise manner. More...
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class | bpp::AbstractSpeciesMultipleSelectionMafStatistics |
| Partial implementation of MafStatistics for method working on multiple distinct subsets of species, in a site-wise manner. More...
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class | bpp::CharacterCountsMafStatistics |
| Compute the base frequencies of a maf block. More...
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class | bpp::SiteFrequencySpectrumMafStatistics |
| Compute the Site Frequency Spectrum of a maf block. More...
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class | bpp::SiteFrequencySpectrumMafStatistics::Categorizer |
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class | bpp::FourSpeciesPatternCountsMafStatistics |
| Compute the frequency of site patterns for a quadruplet of species. More...
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class | bpp::SiteMafStatistics |
| Compute a few site statistics in a maf block. More...
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class | bpp::PolymorphismMafStatistics |
| Counts number of polymorphic / fixed sites in two populations. More...
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class | bpp::SequenceDiversityMafStatistics |
| Provide estimates of sequence diversity. More...
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