supermatrices_get: Create supermatrices from list of alignments and groups...

In AntonelliLab/gaius: Divide and Conquer Phylogenetic Supermatrices and Supertrees in R

Description

Return a supermatrices object from a list of alignments and a groups object.

Usage

supermatrices_get(alignment_list, groups = NULL, column_cutoff = 0.5,
  tip_cutoff = column_cutoff, min_ntips = 5, min_ngenes = 5,
  min_nbps = 200)

sift(x, ...)

## S3 method for class 'supermatrices'
sift(x, keep = NULL, drop = NULL)

Arguments

alignment_list	list of alignments
groups	groups object, determines names of monophyletic groups
column_cutoff	Min. prop. of non-gaps in an alignment column
tip_cutoff	Min. prop. of non-gaps in an alignment row
min_ntips	Min. no. of tips in a supermatrix
min_ngenes	Min. no. of genes in a supermatrix
min_nbps	Min. length (in base pairs) for a gene in a supermatrix
x	supermatrices
keep	Names of matrices to keep, character vector.
drop	Names of matrices to drop, character vector

Value

supermatrices

supermatrices

AntonelliLab/gaius documentation built on June 17, 2020, 8:07 a.m.