makeReference: makeReference

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

makeReference

Description

Function for running the program spades to assemble short read sequencing data

Usage

makeReference(genbank.file = NULL, overwrite = TRUE, rep.origin = FALSE)

Arguments

genbank.file

path to a folder of sequence alignments in phylip format.

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.