getAlignmentPatterns: Rboretum Alignment Pattern Fetcher

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

Rboretum Alignment Pattern Fetcher

Description

Given the path(s) to one or more alignments (and an optional list of taxa), this script returns the site variation pattern for each site (e.g. invariant, biallelic, etc.)

Usage

getAlignmentPatterns(
  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 variation pattern each site in the alignment

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