Efficient Phylogenetics on Large Trees

Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) .


Reference manual

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1.7.2 by Stilianos Louca, 16 days ago

Browse source code at https://github.com/cran/castor

Authors: Stilianos Louca

Documentation:   PDF Manual  

GPL (>= 2) license

Imports parallel, naturalsort, stats, Matrix, RSpectra

Depends on Rcpp

Suggests nloptr

Linking to Rcpp

System requirements: C++11

Imported by dispRity, nichevol.

See at CRAN