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<pre>
/////////////////////////////////////////////////////////////////////////////////////
// //
// INDELible V1.03 control file - rates.txt //
// //
// Adding proportion of invariable sites or gamma rate heterogeneity. //
// //
/////////////////////////////////////////////////////////////////////////////////////
/*
Nucleotide models are used as an example but the principle is exactly the
same for amino-acid models. You just add the [rates] command to a model:
<font color=blue>[rates] pinv alpha ngamcat</font>
This command has no effect in <i>CODON</i> simulations.
* <i>pinv</i> is the proportion of invariable sites (0<=<i>pinv</i><=1).
* <i>alpha</i> is the shape parameter for the gamma distribution (<i>alpha</i>>0).
* If <i>alpha</i>=0 then there will be no gamma rate variation.</li>
* <i>ngamcat</i> is the number of categories to use in the discrete gamma approximation.
* If <i>ngamcat</i>=0 then continuous gamma distribution will be used for rate variation.
* If the command [rates] is not specified all rates will be constant.
*/
<font color=red>[TYPE] NUCLEOTIDE 1</font> // nucleotide simulation using algorithm from method 1
<font color=red>[MODEL] mymodel1 [submodel] JC </font> // JC69 with pinv=0.2 and no gamma
<font color=red> [rates] 0.2 0 0 </font>
<font color=red>[MODEL] mymodel2 [submodel] JC </font> // JC69 with no proportion invariable,
<font color=red> [rates] 0 2 0 </font> // continuous gamma with alpha=2
<font color=red>[MODEL] mymodel3 [submodel] JC </font> // JC69 with no proportion invariable,
<font color=red> [rates] 0 1 10 </font> // 10 category discrete gamma with alpha=1
<font color=red>[MODEL] mymodel4 [submodel] JC </font> // JC69 with pinv=0.2
<font color=red> [rates] 0.2 0.5 0 </font>// continuous gamma with alpha=0.5
<font color=red>[MODEL] mymodel5 [submodel] JC </font> // JC69 with pinv=0.1
<font color=red> [rates] 0.1 1.5 5 </font>// 5 category discrete gamma with alpha=1.5
<font color=red>[TREE] T1 (A:0.1,B:0.1);</font>
<font color=red>[PARTITIONS] Pname1 [T1 mymodel1 1000]</font> // tree T1, model mymodel1, root length 1000
<font color=red>[PARTITIONS] Pname2 [T1 mymodel2 1000]</font> // tree T1, model mymodel2, root length 1000
<font color=red>[PARTITIONS] Pname3 [T1 mymodel3 1000]</font> // tree T1, model mymodel3, root length 1000
<font color=red>[PARTITIONS] Pname4 [T1 mymodel4 1000]</font> // tree T1, model mymodel4, root length 1000
<font color=red>[PARTITIONS] Pname5 [T1 mymodel5 1000]</font> // tree T1, model mymodel5, root length 1000
<font color=red>[EVOLVE] Pname1 10 outputname1</font> // 10 replicates generated from partition Pname1
<font color=red> Pname2 10 outputname2</font> // 10 replicates generated from partition Pname2
<font color=red> Pname3 10 outputname3</font> // 10 replicates generated from partition Pname3
<font color=red> Pname4 10 outputname4</font> // 10 replicates generated from partition Pname4
<font color=red> Pname5 10 outputname5</font> // 10 replicates generated from partition Pname5
</pre>
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