pasta: Ultra-Large Multiple Sequence Alignment with PASTA

In heibl/polenta: Multiple Sequence Alignment with PASTA and GUIDANCE

Description

Provides a complete reimplementation of the PASTA algorithm (Mirarab, Nguyen, and Warnow 2014) in R.

Usage

pasta(seqs, gt, k = 200, msa.program = "mafft", method = "localpair",
  exec, parallel = FALSE, ncore)

Arguments

seqs	An object of class "DNAbin" or "AAbin" containing unaligned sequences of DNA or amino acids.
gt	Currently unused.
k	An integer giving the size of cluster in which the dataset is split.
msa.program	A character string giving the alignment program to use; currently only "mafft" is possible.
method	A character string choosing a method of the alignment program; default is "localpair", see mafft for possible options.
exec	A character string giving the path to the alignment program executable.
parallel	Logical, indicating if the function should be run in parallel or serial mode. Currently unused!
ncore	An integer giving the number of cores to use in parallel mode. Currently unused!

Value

An object of class "polentaDNA".

See Also

extractMSA for extractiong the multiple sequence alignment of a "polentaDNA" object.

heibl/polenta documentation built on May 17, 2019, 3:22 p.m.