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Calculate the number and percentage of parismonyinformative sites in an alignment. Pairwise identity is defined as the number of identicalcolumns (including gaps) between two aligned sequences dividedby the number of columns in the alignment. Summary statisticsare reported unless used with the verbose option in whichall pairwise identities will be reported.
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Treeness is the sum of internal branch lengths divided by the totaltree length. Treeness can beused as a measure of the signal-to-noise ratio in a phylogeny. Calculate summary statistics for terminal branch lengths in a phylogeny. High bipartition support values are thought to be desirable becausethey are indicative of greater certainty in tree topology. This function requires input alignments are in fasta format.Codon alignments are then printed to stdout. Note, pairedsequences are assumed to have the same name between theprotein and nucleotide file.
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