bp_heterogeneity_test1p
A test for distinguishing between selection and population expansion.
Usage
heterogenetity_test -mut_1/--mutsyn
synonymous_mut_count
-mut_2/--mutnon
nonsyn_mut_count
-s/--smaplesize
sample_size
[-i/--iterations
iterations]
[-o/--observed
observed_D]
[-v/--verbose]
[--silent]
[-m/--method
tajimaD
or
fuD]
[--precision]
Description
This is
an
implementation
of
the
Heterogenetity
test
as
described
in
Hahn
MW,
Rausher
MD,
and
Cunningham
CW.
2002.
Genetics
161(1):11-20.
Options
Options in
brackets
above
are
optional
-s
or
--samplesize
samplesize
-mut_1
or
--mutsyn
synonymous
mutation
count
-mut_2
or
--mutnon
nonsynonmous
mutation
count
-i
or
--iterations
number
of
iterations
-o
or
--observed
observed
D
-m
or
--method
tajimaD
or
fuD
for
Tajima's
D
or
Fu
and
Li's
D
-v
or
--verbose
print
out
extra
verbose
messages
--silent
Be
extra
quiet
--precision
Level
of
precision
-
specify
the
number
of
digits
AUTHOR Matthew Hahn <matthew.hahn-at-duke.edu>
For more
information
contact:
Matthew Hahn,
<matthew.hahn-at-duke.edu>
Jason
Stajich
<jason-at-bioperl-dot-org>
Releases
6 releases since Debian 5.0 (Lenny); the text changed 5 times.