Summary:
Given a codon data file, a tree and a codon substitution
model, PositiveSelection performs a series of analyses, along the lines
of Yang, Goldman 2000 paper to identify sites in the data which are under
selective pressure.
Input:
A codon data file in any recognizable
format. Any of the predefined
genetic code translation tables can be used to interpret
the data. A Newick style tree string can either be included in
the data file, or supplied via a separate tree files. Note, that
if a data file contains more than one tree, only the first one
will be read.
The user will be prompted to specify the
cut-off Bayesian level for a site to be considered under selective
pressure (a number between 0 and 1), and how many rate classes
should be used in discretizing continuous distributions.
dN/dS variability is modeled by those 13 distributions.
-
Single Rate no rate variation.
-
Neutral rates are 0 or 1 with mixing parameter P.
-
Selection rates are 0 or 1 or W (estimated) with mixing parameters P1 and P2.
-
Discrete rates are R or R*M1 or R*M2 with mixing parameters P1 and P2.
-
Freqs rates are 0,1/3,2/3,1,3 with mixing parameters P1,P2,P3 and P4.
-
Gamma rates are sampled (by conditional mean) from a two parameter gamma
distribution.
-
2 Gamma rates are sampled (by conditional mean) from a mixture of
a two parameter gamma and a mean 1 gamma.
-
Beta rates are sampled (by conditional mean) from a two parameter beta
distribution (thus the rates are all in [0,1])
-
Beta+w rates are sampled (by conditional mean) from a mixture of a two parameter beta
distribution and the class with rate W.
-
Beta & (Gamma+1) rates are sampled (by conditional mean) from a mixture of a two parameter beta
distribution and a two parameter gamma distribution shifted to [1,Infinity).
-
Beta & (Normal>1) rates are sampled (by conditional mean) from a mixture of a two parameter beta
distribution and a two parameter normal distribution restricted to [1,Infinity).
-
0 & 2 (Normal>1) rates are sampled (by conditional mean) from a mixture of the zero rate class,
a two parameter normal and a mean 1 normal (restricted to [0,Infinity)).
-
3 Normal rates are sampled (by conditional mean) from a mixture of the a mean 0 normal,
a mean 1 normal, and a two-parameter normal, all restricted to [0,Infinity).
The user may choose any combination (or all 13) distributions
to run.
Models: MG94,GY94
with either 3 or 9 frequency parameters codon models can be selected for the analysis.
Output:
A summary table is output to the screen and a detailed report spooled to a file
chosen by the user.
Result
Processing Tools:
None are really applicable.
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