filterAlignments: filterAlignments

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

Description

Function for filtering alignments based on filter summary data

Usage

filterAlignments(
  filter.summary = NULL,
  alignment.data = NULL,
  alignment.folder = NULL,
  format = c("folder", "concatenated"),
  min.alignments = 5,
  overwrite = TRUE
)

Arguments

filter.summary	summary data file from filterSummary
alignment.data	summary data file from alignmentSummary
alignment.folder	folder of alignments to be filtered
format	save format for alignments
min.alignments	minimum number of alignments for a filtered set of data
overwrite	overwrite if file exists?

Value

filters the alignments

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.