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<pre>
/////////////////////////////////////////////////////////////////////////////////////
// //
// INDELible V1.03 control file - basicnucleotide.txt //
// //
// A basic introduction to the structure of the INDELible control file. //
// //
/////////////////////////////////////////////////////////////////////////////////////
// It is useful to know that anything on a line after two forward slashes is ignored.
/*
Another useful thing to know is that anything after a forward slash and star
is ignored until INDELible sees a star followed by a forward slash later on.
*/
<font color=red>[TYPE] NUCLEOTIDE 1</font> // EVERY control file must begin with a [TYPE] command.
// The number after "NUCLEOTIDE" can be 1 or 2 and chooses the
// algorithm that INDELible uses (see manuscript). Both give
// identical results but in some cases one is quicker.
// Other blocks and commands following this statement
// can come in any order you like.
<font color=red>[MODEL] modelname</font> // Evolutionary models are defined in [MODEL] blocks.
<font color=red> [submodel] JC </font>// Here the substitution model is simply set as JC69.
<font color=red> [indelmodel] NB 0.4 1</font> // Geometric indel length distribution (q=0.4, r=1)
<font color=red> [insertrate] 0.08 </font> // insertion rate = 0.08 relative to substitution rate of 1
<font color=red> [deleterate] 0.12 </font>// deletion rate = 0.12 relative to substitution rate of 1
<font color=red>[TREE] treename (A:0.1,B:0.1);</font> // User trees are defined here
<font color=red>[PARTITIONS] partitionname </font> // [PARTITIONS] blocks say which models go with
<font color=red> [treename modelname 1000]</font> // which trees and define the length of the
// sequence generated at the root (1000 here).
<font color=red>[EVOLVE] partitionname 100 outputname</font> // This will generate 100 replicate datasets
// from the [PARTITIONS] block named above.
// The true alignment will be output in a file named outputname_TRUE.phy
// The unaligned sequences will be output in a file named outputname.fas
// To learn how to implement more complicated simulations (or different
// models) please consult the manual or the other example control files.
</pre>
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