write.msa: Writing MSA Objects to Files

In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description

Writes a multiple sequence alignment (MSA) object to a file in one of several formats.

Usage

write.msa(x, file=NULL,
format=ifelse((f <- guess.format.msa(file, method="extension"))=="UNKNOWN", "FASTA", f),
pretty.print=FALSE)

Arguments

x	an object of class msa
file	File to write (will be overwritten). If NULL, output goes to terminal.
format	format to write MSA object. Valid values are "FASTA", "PHYLIP", "MPM", or "SS".
pretty.print	Whether to pretty-print alignment (turning bases which match the first base in the same column to ".").

Note

pretty.print does not work if format="SS".

Author(s)

Melissa J. Hubisz and Adam Siepel

rphast documentation built on May 1, 2019, 9:26 p.m.