Man pages for Hackout3/saphy
Sequential Analysis of Phylogenies

branchLengthMetricsProduces a dataframe of tree branch length statistics
compute.distance.matrixComputes a pairwise distance matrix
expand.distance.matrixUpdates a pre-existing distance matrix
imbalanceMetricsProduces a dataframe of tree imbalance statistics
imbalanceThresholdProduces a list of a confidence intervals given a tree...
pairwise.distanceCalculate pairwise distance between two sequences
permuteTreesProduces a list of permuted trees with the same tip and...
plot.branch.lengthsPlots the average branch lengths over time
prunePermuteProduces a list of a list of sequentially growing trees given...
simulatetreeSimulate tree and sequences in two-population SIR-model
timeprunePrune tree in time order
tiplengthExtracts the length of a tip from a tree
Hackout3/saphy documentation built on May 6, 2019, 10:52 p.m.