concatenateAlignments: concatenateAlignments

In chutter/FilterZone: R Package For Detecting the Anomaly Zone and Alignment Filtering in Large Phylogenomic Datasets

Description

Function for concatenating a large number of alignments

Usage

concatenateAlignments(
  alignment.folder = NULL,
  file.name = NULL,
  output.dir = NULL,
  partition.format = c("raxml", "table")
)

Arguments

alignment.folder	folder that contains aligmnents to be concatenated
file.name	output file name
output.dir	directory to save file to
partition.format	partition file format. Can select both.

Value

saves to file concatenated alignments and partition files delimiting the coordinates of each indidividual marker

Examples

your.tree = ape::read.tree(file = "file-path-to-tree.tre")
astral.data = astralPlane(astral.tree = your.tree,
                          outgroups = c("species_one", "species_two"),
                          tip.length = 1)

chutter/FilterZone documentation built on Dec. 19, 2021, 4:07 p.m.