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<pre>
/////////////////////////////////////////////////////////////////////////////////////
// //
// INDELible V1.03 control file - NUCLEOTIDE.txt //
// //
// An introduction to different nucleotide substitution models. //
// //
/////////////////////////////////////////////////////////////////////////////////////
/* Again - the control file must begin with the [TYPE] statement */
<font color=red>[TYPE] NUCLEOTIDE 2</font> // nucleotide simulation using algorithm from method 2.
/* Many different models can be defined in a single control file */
<font color=red>[MODEL] JCexample</font>
<font color=red> [submodel] JC </font> // JC69
<font color=red>[MODEL] HKYexample</font>
<font color=red> [submodel] HKY 2.5 </font> // HKY with a=f=kappa=2.5, b=c=d=e=1
<font color=red> [statefreq] 0.4 0.3 0.2 0.1 </font> // pi_T=0.4, pi_C=0.3, pi_A=0.2, pi_G=0.1
<font color=red>[MODEL] K81example</font>
<font color=red> [submodel] K81 1.5 2.5 </font> // K81 with b=e=1.5, c=d=2.5, a=f=1
<font color=red>[MODEL] GTRexample</font>
<font color=red> [submodel] GTR 0.2 0.4 0.6 0.8 1.2</font> // GTR: a=0.2, b=0.4, c=0.6, d=0.8, e=1.2, f=1
<font color=red> [statefreq] 0.1 0.2 0.3 0.4 </font> // pi_T=0.1, pi_C=0.2, pi_A=0.3, pi_G=0.4
/* Many different trees can be defined in a single control file */
<font color=red>[TREE] t1 (A:0.1,B:0.1);</font>
<font color=red>[TREE] t2 ( (A:0.1, B:0.1):0.1, (C:0.3, D:0.3):0.5 );</font>
<font color=red>[TREE] t3 ( species1:0.1, species2:0.1, (species3:0.2, species4:0.2):0.01 );</font>
<font color=red>[TREE] t4
(((1:0.1,2:0.1):0.1,(3:0.1,4:0.1):0.1):0.1,((5:0.1,6:0.1):0.1,(7:0.1,8:0.1):0.1):0.1);</font>
/* Many different partition groupings can be defined in a single control file */
<font color=red>[PARTITIONS] pJC [t1 JCexample 1600]</font> // tree t1, model JCexample, root length of 1600
<font color=red>[PARTITIONS] pHKY [t2 HKYexample 500]</font> // tree t2, model HKYexample, root length of 500
<font color=red>[PARTITIONS] pK81 [t3 K81example 988]</font> // tree t3, model K81example, root length of 988
<font color=red>[PARTITIONS] pGTR [t4 GTRexample 754]</font> // tree t4, model GTRexample, root length of 754
/* The [EVOLVE] statement is then used to list all the simulations you want to do */
<font color=red>[EVOLVE] </font>
<font color=red>pJC 500 JCout</font> // 500 replicates generated from partition pJC in file JCout.fas etc
<font color=red>pHKY 50 HKYout</font> // 50 replicates generated from partition pHKY in file HKYout.fas etc
<font color=red>pK81 25 K81out</font> // 25 replicates generated from partition pK81 in file K81out.fas etc
<font color=red>pGTR 10 GTRout</font> // 10 replicates generated from partition pGTR in file GTRout.fas etc
/////////////////////////////////////////////////////////////////////////////////////
/*
All nucleotide substitution models (apart from UNREST) are specified in
relation to this general substitution rate matrix:
TO
---------------------------------------------
FROM || T | C | A | G
------++----------+----------+----------+-----------
T || - | a Pi_C | b Pi_A | c Pi_G
C || a Pi_T | - | d Pi_A | e Pi_G
A || b Pi_T | d Pi_C | - | f Pi_G
G || c Pi_T | e Pi_C | f Pi_A | -
where Pi_T, Pi_C, Pi_A, Pi_G are the stationary base frequencies.
The different models are specified using the commands listed below in blue
(the names correspond to those used by <a href="http://darwin.uvigo.es/software/modeltest.html" target="_blank">Modeltest</a>):</li>
+-----+----------------------------------+----------------------------------+
| <b> N </b> | <b>Usage </b> | <b>Notes </b> |
+-----+----------------------------------+----------------------------------+
| 0 | <font color=blue> [submodel] JC </font> | a=b=c=d=e=f=1 |
| 1 | <font color=blue> [submodel] F81 </font> | a=b=c=d=e=f=1 |
+-----+----------------------------------+----------------------------------+
| 2 | <font color=blue> [submodel] K80 a </font> | a=f=kappa, b=c=d=e=1 |
| 3 | <font color=blue> [submodel] HKY a </font> | a=f=kappa, b=c=d=e=1 |
+-----+----------------------------------+----------------------------------+
| 4 | <font color=blue> [submodel] TrNef a f </font> | a=kappa1, f=kappa2, b=c=d=e=1 |
| 5 | <font color=blue> [submodel] TrN a f </font> | a=kappa1, f=kappa2, b=c=d=e=1 |
+-----+----------------------------------+----------------------------------+
| 6 | <font color=blue> [submodel] K81 b c </font> | b=e, c=d, a=f=1 |
| 7 | <font color=blue> [submodel] K81uf a b c d e </font> | b=e, c=d, a=f=1 |
+-----+----------------------------------+----------------------------------+
| 8 | <font color=blue> [submodel] TIMef a b c </font> | b=e, c=d, f=1 |
| 9 | <font color=blue> [submodel] TIM a b c </font> | b=e, c=d, f=1 |
+-----+----------------------------------+----------------------------------+
| 10 | <font color=blue> [submodel] TVMef b c d e </font> | a=f=1 |
| 11 | <font color=blue> [submodel] TVM b c d e </font> | a=f=1 |
+-----+----------------------------------+----------------------------------+
| 12 | <font color=blue> [submodel] SYM a b c d e </font> | f=1 |
| 13 | <font color=blue> [submodel] GTR a b c d e </font> | f=1 |
+-----+----------------------------------+----------------------------------+
| 14 | <font color=blue> [submodel] F84ef k </font> | b=c=d=e=1, a=(1+k/Y), f=(1+k/R) |
| 15 | <font color=blue> [submodel] F84 k </font> | b=c=d=e=1, a=(1+k/Y), f=(1+k/R) |
| | | N.B. Y=pi_T+pi_C , R=pi_A+pi_G |
+-----+----------------------------------+--------------------------+-------+
| 16 | <font color=blue> [submodel] UNREST TC TA TG CT CA CG AT AC AG GT GC</font> | GA=1 |
+-----+-------------------------------------------------------------+-------+
N.B. <i>N</i> can be substituted for the model name.
e.g. <font color=blue>[submodel] 0</font> instead of <font color=blue>[submodel] JC</font>
For the models with even N (0-16) the base frequencies are set automatically.
For models with odd N (1-15) the base frequencies are given using the command:
<font color=blue>[statefreq] Pi_T Pi_C Pi_A Pi_G</font>
*/
</pre>
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