prune.tree: Prune a Tree
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Value Author(s) Examples

Prune sequences from a file

1	prune.tree(tree, seqs, all.but = FALSE)

`tree`	A vector of character strings, each containing a newick tree
`seqs`	The sequences to prune from the trees
`all.but`	A logical value. If false, prunes all the named sequences from the tree. If TRUE, prunes all sequences except the ones named.

a vector of character strings representing the pruned trees.

Melissa J. Hubisz and Adam Siepel

trees <- c("((hg18, panTro2), mm9);",
           "((hg18:0.142679,(mm9:0.083220,rn4:0.090564):0.269385):
                0.020666,canFam2:0.193569);")
prune.tree(trees, c("panTro2", "mm9"), all.but=TRUE)
prune.tree(trees, "hg18", all.but=FALSE)