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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML>
<HEAD>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<META NAME="Author" CONTENT="Karen Gershowitz">
<META NAME="GENERATOR" CONTENT="Mozilla/4.08 [en] (Win95; U) [Netscape]">
<link REL="SHORTCUT ICON" HREF="favicon.ico" type="image/x-icon">
<TITLE>instructions</TITLE>
</HEAD>
<BODY TEXT="#000000" BGCOLOR="#FFFFFF" LINK="#0000EE" VLINK="#551A8B" ALINK="#FF0000">
<FONT COLOR="#FF0000"><FONT SIZE=+1>Instructions for using
the heterogeneity test</FONT></FONT>
<p>I am currently only distributing the original Unix version of this software, as other implementations were dependent on old versions of OSX.</p>
<p>The first step in running the program is saving the 'make_trees.txt' file you downloaded as 'make_trees.pl'.</p>
<P>In order to run the program you need to supply four simple numbers:
<P>1. Number of sampled sequences/chromosomes (designated "<FONT COLOR="#FF0000">s</FONT>")
<BR>2. Number of segregating sites of your putatively neutral class (Synonymous
mutations would be an obvious choice, but you could use others like non-binding
sites in promoters; designated "<FONT COLOR="#FF0000">mut_1</FONT>")
<BR>3. Number of seg. sites of your selected class (usually nonsynonymous,
but could be e.g. binding sites; designated "<FONT COLOR="#FF0000">mut_2</FONT>")
<BR>4. Difference in D values. The perl program will run with either
Tajima's D or Fu and Li's D, and you need to get those values for your
neutral and selected classes separately and then the difference = (Dneutral
- Dselected). (designated "<FONT COLOR="#FF0000">observed</FONT>")
<P>All of this was spelled out in the old Mac OSX version, but you need to know these tags to run it at the command line.
<p></p>
<p>So the simple command line argument looks like this ("<FONT COLOR="#FF0000">i</FONT>"
is the number of iterations you want it to run):
</p>
<P><FONT COLOR="#FF6600">perl make_trees.pl -s 10 -mut_1 10
-mut_2 5 -observed 1.2 -i 1000 -method tajimaD</FONT>
<P>The other method is called "<FONT COLOR="#FF0000">fuD</FONT>".
The output line will be a bit confusing at first. The thing you want
to know is the "index". This tells you where in the distribution
your observed is closest to (actually, just smaller than). One output
line from the above input looks like this:
<P><FONT COLOR="#FF0000">index 941 value=1.2099 out of 1000 total (obs=1.2000)</FONT>
<P>So the p-value is [(total-index)/total] (=.059) for a one-tailed test. Or, if you get a value in the other extreme (i.e. the reported "index" is close to zero), the p-value would be [(index/total)].<BR>
<P>Make sure you read the paper and know what the program does before running
it!
</BODY>
</HTML>