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/////////////////////////////////////////////////////////////////////////////////////
// //
// 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.
*/
[TYPE] NUCLEOTIDE 1 // 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.
[SETTINGS]
[randomseed] 1568746 // seed for random generator so outputs can be checked
[MODEL] modelname // Evolutionary models are defined in [MODEL] blocks.
[submodel] JC // Here the substitution model is simply set as JC69.
[indelmodel] NB 0.4 1 // Geometric indel length distribution (q=0.4, r=1)
[insertrate] 0.08 // insertion rate = 0.08 relative to substitution rate of 1
[deleterate] 0.12 // deletion rate = 0.12 relative to substitution rate of 1
[TREE] treename (A:0.1,B:0.1); // User trees are defined here
[PARTITIONS] partitionname // [PARTITIONS] blocks say which models go with
[treename modelname 20] // which trees and define the length of the
// sequence generated at the root (20 here).
[EVOLVE] partitionname 5 outputname // This will generate 5 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.
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