prepareAlignments: prepareAlignments

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

prepareAlignments

Description

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

Usage

prepareAlignments(
  contig.folder = NULL,
  genbank.file = NULL,
  blast.path = "blast",
  overwrite = FALSE,
  quiet = TRUE
)

Arguments

contig.folder	path to a folder of sequence alignments in phylip format.
genbank.file	contigs are added into existing alignment if algorithm is "add"
blast.path	algorithm to use: "add" add sequences with "add.contigs"; "localpair" for local pair align. All others available
overwrite	TRUE to supress screen output
quiet	TRUE to supress screen output
out.dir	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.