internal

ape-internal

ape provides functions for reading, writing, plotting, and
        manipulating phylogenetic trees, analyses of comparative data
        in a phylogenetic framework, ancestral character analyses,
        analyses of diversification and macroevolution, computing
        distances from allelic and nucleotide data, reading and writing
        nucleotide sequences, and several tools such as Mantel's test,
        minimum spanning tree, generalized skyline plots, graphical
        exploration of phylogenetic data (alex, trex, kronoviz),
        estimation of absolute evolutionary rates and clock-like trees
        using mean path lengths and penalized likelihood. Phylogeny
        estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and
        triangle methods, and several methods handling incomplete
        distance matrices (NJ*, BIONJ*, MVR*, and the corresponding
        triangle method). Some functions call external applications
        (PhyML, Clustal, T-Coffee, Muscle) whose results are returned
        into R.

ape-internal: Internal Ape Functions

Description

Arguments