1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
|
<!--#include file="files/top.html" -->
<pre>
/////////////////////////////////////////////////////////////////////////////////////
// //
// INDELible V1.03 control file - AMINOACID.txt //
// //
// An introduction to different amino-acid substitution models. //
// //
/////////////////////////////////////////////////////////////////////////////////////
/* Again - the control file must begin with the [TYPE] statement */
<font color=red>[TYPE] AMINOACID 1</font> // amino-acid simulation using algorithm from method 1.
/* Many different models can be defined in a single control file */
<font color=red>[MODEL] JTTexample1</font>
<font color=red> [submodel] JTT </font> // JTT model defined using the code.
<font color=red>[MODEL] JTTexample2</font>
<font color=red> [submodel] 1 </font> // JTT model defined using a number.
<font color=red>[MODEL] WAGexample</font>
<font color=red> [submodel] WAG </font> // WAG defined using the code
/* Specifying stationary frequencies will force the +F version of a model */
<font color=red>[MODEL] WAG_Fexample</font>
<font color=red> [submodel] WAG </font> // WAG+F
<font color=red> [statefreq] </font> // list of 20 numbers
<font color=red> 0.079066 0.055941 0.041977 0.053052 0.012937 </font> // A R N D C
<font color=red> 0.040767 0.071586 0.057337 0.022355 0.062157 </font> // Q E G H I
<font color=red> 0.099081 0.064600 0.022951 0.042302 0.044040 </font> // L K M F P
<font color=red> 0.061197 0.053287 0.012066 0.034155 0.069147 </font> // S T W Y V
/* User defined (reversible) amino-acid substitution model */
<font color=red>[MODEL] USERexample</font> // e.g. formatted like <a href="userAAmodel.txt" target="_blank">this</a>
<font color=red> [submodel] userAAmodel.txt </font> // for the Dayhoff-dcmut model.
/* 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] pJTT1 [t1 JTTexample1 160]</font> // tree t1, model JTTexample1, root length 160
<font color=red>[PARTITIONS] pJTT2 [t2 JTTexample2 500]</font> // tree t2, model JTTexample2, root length 500
<font color=red>[PARTITIONS] pWAG1 [t3 WAGexample 988]</font> // tree t3, model WAGexample, root length 988
<font color=red>[PARTITIONS] pWAG2 [t4 WAG_Fexample 75]</font> // tree t4, model WAG_Fexample, root length 75
<font color=red>[PARTITIONS] pUSER [t3 USERexample 988]</font> // tree t3, model USERexample, root length 988
/* The [EVOLVE] statement is then used to list all the simulations you want to do */
<font color=red>[EVOLVE] </font>
<font color=red>pJTT1 40 J1out</font> // 40 replicates generated from partition pJTT1 in file J1out.fas etc
<font color=red>pJTT2 50 J2out</font> // 50 replicates generated from partition pJTT2 in file J2out.fas etc
<font color=red>pWAG1 25 Wout</font> // 25 replicates generated from partition pWAG1 in file Wout.fas etc
<font color=red>pWAG2 10 WFout</font> // 10 replicates generated from partition pWAG2 in file WFout.fas etc
<font color=red>pUSER 13 Uout</font> // 13 replicates generated from partition pUSER in file Uout.fas etc
/////////////////////////////////////////////////////////////////////////////////////
/*
All amino-acid substitution models are specified as: <font color=blue>[submodel] value</font>
where <b>value</b> is just an integer <b>N</b> or a <b>code</b> used to pick the amino-acid
substitution model as defined below (references given where appropriate):
+-----+---------------+-------------------------------+
| <b>N</b> | <b>code</b> | <b>Reference</b> |
+-----+---------------+-------------------------------+
| 0 | Poisson | n/a |
| 1 | JTT | Jones et al,. 1992 |
| 2 | JTT-dcmut | Kosiol and Goldman, 2005 |
| 3 | Dayhoff | Dayhoff et al., 1978 |
| 4 | Dayhoff-dcmut | Kosiol and Goldman, 2005 |
| 5 | WAG | Whelan and Goldman, 2001 |
| 6 | mtMAM | Yang et al., 1998 |
| 7 | mtART | Abascal et al., 2007 |
| 8 | mtREV | Adachi and Hasegawa, 1996 |
| 9 | rtREV | Dimmic et al., 2002 |
| 10 | cpREV | Adachi, 2000 |
| 11 | Vt | Muller and Vingron, 2000 |
| 12 | Blosum | Henikoff and Henikoff, 1992 |
| 13 | LG | Le and Gascuel, 2008 |
| 14 | HIVb | Nickle et al., 2007 |
| 15 | HIVw | Nickle et al., 2007 |
| 16 | USER | n/a |
+-----+---------------+-------------------------------+
The only exception is the user-model where you simply specify the
name of the file that contains the state frequencies and the rate
matrix Q. This file should be in the same folder as INDELible.
*/
</pre>
<!--#include file="files/bottom.html" -->
|
