getAlignmentBreakdown: Rboretum Alignment Breaker Downer

In BobLiterman/Rboretum: Compare Phylogenetic Trees and Alignment Support Values

Rboretum Alignment Breaker Downer

Description

Given the path(s) to one or more alignments (and an optional list of taxa), this script returns a full breakdown of alignment statistics (including

Usage

getAlignmentBreakdown(
  alignment_path,
  species_info,
  use_gaps,
  alignment_name,
  prefix,
  suffix
)

Arguments

alignment_path	Where to find alignment files. Options include: A character vector of one or more alignment file paths (relative or absolute) A path to a single directory containing all alignment files (relative or absolute)
species_info	OPTIONAL: List of taxa to analyze [Default: Process alignment using all taxa if solo, all shared in multiple]. Can be provided as: phylo object from which species will be extracted; or multiPhylo object from which common species will be extracted; or Character vector with 3+ taxon IDs Semicolon-separated list of taxon IDs
use_gaps	OPTIONAL: If FALSE, treat gaps as missing data (like N) [Default: TRUE, treat gaps as indel data]
alignment_name	OPTIONAL: Chacter vector of names for each alignment. If missing or incomplete, the base filename of the alignment is used
prefix	OPTIONAL: If 'alignment_path' is a directory, provide a character vector of file prefixes (e.g. all alignment files start with "Mafft_")
suffix	OPTIONAL: If 'alignment_path' is a directory, provide a character vector of file suffixes (e.g. all alignment files end with ".phy")

Value

Dataframe containing a breakdown of alignment statistics

BobLiterman/Rboretum documentation built on July 6, 2023, 7:46 p.m.