findORF: findORF

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

findORF

Description

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

Usage

findORF(input.seq = NULL, codons = F, min.size = 80)

Arguments

input.seq	path to a folder of sequence alignments in phylip format.
codons	algorithm to use: "add" add sequences with "add.contigs"; "localpair" for local pair align. All others available
min.size	TRUE to supress screen output
genbank.file	contigs are added into existing alignment if algorithm is "add"

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.