polenta: polenta: PASTA Optimal confidENce Transivitiy Alignment

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

Description

Multiple Sequence Alignment with PASTA and GUIDANCE: PASTA (Mirarab, Nguyen, and Warnow 2014) is a highly accurate and scalable algorithm for multiple sequence alignment. GUIDANCE (Penn, Privman, Landan, Grauer, and Pupko 2010) is a well-performing method for the assessment of alignment uncertainty. Both methods are available as stand-alone programs, but, unfortunately, cannot be combined. This package provides a reimplementation of PASTA and GUIDANCE to combine their power to accurately align large numbers of sequences.

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

Usage

polenta(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.