set.alignment.file: Defines alignment file but does not read it, then call...

In phraber/lassie: Tools to select sites and sequences that represent variation in a longitudinally sampled protein alignment

Description

Reading the alignment file is done by prep.aln for control of excise.refseq status.

Usage

set.alignment.file(S, f, pngs2o = NULL, alignment_format = "fasta")

Arguments

S	swarmtools object
f	alignment file
pngs2o	option to indicate whether or not to mark PNG Ns as O.
alignment_format	Format of alignment file/s; must be one of these: "fasta", "clustal", "phylip", "msf", or "mase".

Value

swarmtools object with defined aas_aln, refseq_lut, and tf_loss if possible

phraber/lassie documentation built on May 25, 2019, 6:01 a.m.