buildMitogenomes: buildMitogenomes

In chutter/MitoCap: Package For extracting, assembling, annotating and aligning mitochondrial genomes from high-throughput sequencing data

buildMitogenomes

Description

Function for batch trimming a folder of alignments, with the various trimming functions available to select from

Usage

buildMitogenomes(
  annotation.dir = "Annotations",
  alignment.folder = "Alignments/untrimmed-alignments",
  genome.alignment = "Genomes/alignments/untrimmed_mitogenome_alignment.phy",
  genome.dir = "Genomes",
  output.dir = NULL,
  overwrite = FALSE
)

Arguments

annotation.dir	path to a folder of sequence alignments in phylip format.
alignment.folder	path to a folder of sequence alignments in phylip format.
genome.alignment	available input alignment formats: fasta or phylip
genome.dir	contigs are added into existing alignment if algorithm is "add"
output.dir	available output formats: phylip
overwrite	TRUE to supress mafft screen output

Value

an alignment of provided sequences in DNAStringSet format. Also can save alignment as a file with save.name

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/MitoCap documentation built on July 17, 2025, 12:04 a.m.