filterGeneTrees: filterGeneTrees

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

Description

Filters gene trees using provided filtration and alignment data

Usage

filterGeneTrees(
  filter.summary = NULL,
  alignment.data = NULL,
  genetree.folder = NULL,
  format = c("folder", "concatenated"),
  overwrite = TRUE,
  taxa.remove = NULL,
  min.trees = 5,
  min.n.samples = 4,
  min.sample.prop = NULL,
  make.polytomy = TRUE,
  polytomy.limit = 0,
  remove.node.labels = FALSE
)

Arguments

filter.summary	summary data file from filterSummary
alignment.data	summary data file from alignmentSummary
genetree.folder	your target folder of gene trees that correspond to the alignments being filtered
format	save format for genetrees
overwrite	overwrite if file exists?
taxa.remove	species that you would like removed from each gene tree
min.trees	mimimum number of trees to keep filtered set
min.n.samples	the minimum number of samples to keep a gene tree
min.sample.prop	the minimum proportion of samples to keep a gene tree
polytomy.limit	the value at which to collapse a node into a polytomy
remove.node.labels	strips trees of node labels if downstream analyses give you trouble (not recommended)
collapse.polytomy	collapses polytomies in the gene trees

Value

filters gene trees either in a folder or concatenated set of trees

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.