alignerTrimmer: alignerTrimmer

In gehara/Junkyardtools: Toolbox for genetic junkyard survival

Description

This function aligns and trims all fasta sequences present in a directory

Usage

alignerTrimmer(path.to.fasta = getwd(), samples.cutoff = 10,
  quantile.cutoff = 0.25, segsites.cutoff = 0.5, remove.gaps = T,
  input.id.name = "uce-", output.prefix = "ALTRIM_",
  output.dir = "OUT")

Arguments

path.to.fasta	character string. path to the directory of fasta files.
samples.cutoff	integer. Exclude loci that have less samples than the sample.cutoff.
quantile.cutoff	float. Exclude all sequences with length bellow the quantile of the distribution of lengths across all samples. This is to exclude samples with short sequences before trimming.
segsites.cutoff	float. Exclude locus if the number segsites is larger than the segsites.cutoff of total length of the alignment.
remove.gaps	logical. If TRUE remove gaps and trim alignment.
input.id.name	character string. Text indicating a wildcard to find the loci to process.
output.prefix	character string. Text prefix to identify the output.
output.dir	character string. Path to the output directory.

Value

processed sequence alignmnents to the to the output directory.

Author(s)

Marcelo Gehara and Edward Myers

gehara/Junkyardtools documentation built on Nov. 4, 2019, 1:04 p.m.