summarizeAlignments: summarizeAlignments

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

Description

Function for gather summary statistics on your alignment. Can be used for filtering or summarizing data.

Usage

summarizeAlignments(
  alignment.path = NULL,
  file.export = NULL,
  dataset.name = NULL,
  alignment.type = "phylip"
)

Arguments

alignment.path	path to a folder of sequence alignments in phylip format.
file.export	give a save name if you wnat to save the summary to file.
dataset.name	A name for your dataset. i.e. exons, introns, UCEs
alignment.type	select the format of the alignment. Phylip is avaialble for now, will be expanded in the future.

Value

returns a data.table with the raw summary statistics calculated for each alignment in the alignment.path. A csv file can optionally be saved by giving a file name to file.export

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.