[R] function to compute consensus DNA sequence by plurality?

[Kim Milferstedt]

Hello,

I am looking for a function that computes a consensus DNA sequence by 
plurality. I found "consensus" in bio3d which almost does what I need.
However, it would be important for me to include ambiguities and not to 
omit every position that is less than the threshold set in "consensus".

Is anybody aware of a package with a function that includes ambiguities 
in a consensus sequence?

Thanks already!

Kim

Here are a couple of sequences to illustrate what I would like:

TGCATACACCGACAACATCCTCGACGACTACACCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
AGCATACACCGACAACATCCTCGATGACTACTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
AGCATACACCGACAACATCCTCGATGACTACTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG

  GC TACACC AC A  TCCT GA GACT CTGCTACTACG
#This is what I get from "consensus" in bio3d with a threshold of 0.85.

HGCMTACACCRACRAYRTCCTSGAYGACTWCTGCTACTACG
# This is what I would like to get.


___________________________________________
Kim Milferstedt, PhD
Postdoctoral Researcher
University of Illinois at Urbana-Champaign
Department of Microbiology
C207 CLSL
601 S. Goodwin Avenue
Urbana, IL 61801

phone: 001-217-244-0721
email: milferst at uiuc.edu