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********************************************************************************
INDELible V1.03 by Will Fletcher : Simulation began at: Fri Jun 12 01:59:44 2020
********************************************************************************
* Block 1 was completed in 0.013479 seconds.
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* Block 2 was completed in 0.022621 seconds.
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* Block 3 was completed in 0.033144 seconds.
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* Block 4 was completed in 0.06046 seconds.
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* Block 5 was completed in 0.043499 seconds.
********************************************************************************
* Simulation completed. Whole batch took: 0.178116 seconds.
INDELible V1.03 Simulations completed at: Fri Jun 12 01:59:44 2020
********************************************************************************
Original Control File
-----------------------
/////////////////////////////////////////////////////////////////////////////////////
// //
// INDELible V1.03 control file - CODONsites.txt //
// //
// An introduction to different codon site models. //
// //
/////////////////////////////////////////////////////////////////////////////////////
/* Again - the control file must begin with the [TYPE] statement */
[TYPE] CODON 1 // codon simulation using algorithm from method 1
[SETTINGS]
[randomseed] 1568746 // seed for random generator so outputs can be checked
/* Many different models can be defined in a single control file */
[MODEL] M0example
[submodel] 2.5 0.5 // kappa=2.5, w=0.5
[MODEL] M1example
[submodel] 2.5 // kappa=2.5
0.2 // p0=0.2, p1=0.8
0.5 1 // w0=0.5, w1=1
[MODEL] m1example
[submodel] 2.5 0.2 0.5 1 // same as above, but can be on one line
[MODEL] M2example
[submodel] 2.0 // kappa=2
0.2 0.3 // p0=0.2, p1=0.3, p2=0.5
0.5 1.0 2.0 // w0=0.5, w1=1, w2=2
[MODEL] M3example
[submodel] 2.5 // kappa=2.5
0.05 0.10 0.20 0.30 0.25 // p0, p1, p2, p3, p4, p5=0.1
0.13 0.72 1.38 2.74 5.42 10.23 // w0, w1, w2, w3, w4, w5
[MODEL] M4example
[submodel] 2.5 // kappa=2.5
0.05 0.1 0.2 0.3 // p0, p1, p2, p3, p4=0.35
0 0.333333 0.666666 1 3 // w0, w1, w2, w3, w4
[TREE] t1 (A:0.1,B:0.1);
/* Many different partition groupings can be defined in a single control file */
[PARTITIONS] pM0 [t1 M0example 20] // tree t1, model M0example, root length 20
[PARTITIONS] pM1 [t1 M1example 20] // tree t1, model M1example, root length 20
[PARTITIONS] pM2 [t1 M2example 20] // tree t1, model M2example, root length 20
[PARTITIONS] pM3 [t1 M3example 20] // tree t1, model M3example, root length 20
[PARTITIONS] pM4 [t1 M4example 20] // tree t1, model M4example, root length 20
/* The [EVOLVE] statement is then used to list all the simulations you want to do */
[EVOLVE]
pM0 5 out1 // 5 replicates generated from partition pM0 in file out1.fas etc
pM1 5 out2 // 5 replicates generated from partition pM1 in file out2.fas etc
pM2 5 out3 // 5 replicates generated from partition pM2 in file out3.fas etc
pM3 5 out4 // 5 replicates generated from partition pM3 in file out4.fas etc
pM4 5 out5 // 5 replicates generated from partition pM4 in file out5.fas etc
///////////////////////////////////////////////////////////////////////////////////
/*
The command is [submodel] ECMunrest for the empirical unrestricted model.
The command is [submodel] ECMrest for the empirical restricted model.
The non-empirical codon substitution models are all special cases of M3.
They are specified using the following format for a model with K categories:
M3 (discrete) // p(K-1)=1-p(K-2)-...-p1-p0
[submodel] kappa
p0 p1 ... p(K-2) // proportions
ω0 ω1 ... ω(K-2) ω(K-1) // omegas
All models M0-M13 can be represented in this M3 format, e.g.
M0 (one-ratio)
[submodel] kappa &omega0 // p0=1
M1 (neutral)
[submodel] kappa p0 ω0 1 // ω1=1; p1=1-p0
M2 (selection)
[submodel] kappa p0 p1 ω0 1 ω2 // ω1=1; p2=1-p1-p0
M4 (freqs) with K=5
[submodel] kappa
p0 p1 p2 p3 // p4=1-p3-p2-p1-p0
0 0.333333 0.666666 1 3 // ω0, ω1, ω2, ω3, ω4
A script (named "M5-13") is provided with INDELible to calculate the discrete
values for this command from the parameters used in models M5-M13.
Codon frequencies are changed from being equal by listing 64 numbers
(separated by white space) after the command [statefreq].
*/
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