mafft.merge {ips}

Profile Alignment with MAFFT

Description

Merge two or more DNA or amino acid sequence alignments by profile alignment with MAFFT.

Usage

mafft.merge(subMSA, method = "auto", gt, thread = -1, exec, quiet = TRUE)

Arguments

subMSA

A list of objects of class "DNAbin" or "AAbin".

method

A character string giving the alignment method. Available accuracy-oriented methods for less than 200 sequences are "localpair", "globalpair", and "genafpair"; "retree 1" and "retree 2" are for speed-oriented alignment. The default is "auto", which lets MAFFT choose an appropriate alignment method.

gt

An object of class phylo that is to be used as a guide tree during alignment.

thread

Integer giving the number of physical cores MAFFT should use; with thread = -1 the number of cores is determined automatically.

exec

A character string giving the path to the MAFFT executable including its name, e.g. something like /user/local/bin/mafft under UNIX-alikes.

quiet

Logical, if set to TRUE, mafft progress is printed out on the screen.

Value

An object of class "DNAbin" or "AAbin".