polenta_dev: 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

polenta_dev(seqs, gt, k = 200, bootstrap = 100, method = "auto", exec,
  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.
bootstrap	An integer giving the number of bootstrap replicates.
method	A character string choosing a method of the alignment program; see mafft for possible options.
exec	A character string giving the path to the alignment program executable.
ncore	An integer giving the number of cores to use in parallel mode.

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.