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/////////////////////////////////////////////////////////////////////////////////////
// //
// INDELible V1.03 control file - CODON.txt //
// //
// An introduction to codon substitution models. //
// //
/////////////////////////////////////////////////////////////////////////////////////
/* Again - the control file must begin with the [TYPE] statement */
[TYPE] CODON 2 // codon simulation using algorithm from method 2
[SETTINGS]
[randomseed] 1568746 // seed for random generator so outputs can be checked
/* Many different models can be defined in a single control file */
[MODEL] M0example1
[submodel] 2.5 0.5 // kappa=2.5, w=0.5
[MODEL] M0example2
[submodel] 5.0 1.0 // kappa=5.0, w=1.0
/* The genetic code is the standard code by default but can be changed, e.g. */
[MODEL] M0example3
[submodel] 2.5 0.5 // kappa=2.5, w=0.5
[geneticcode] 3 // The Yeast Mitochondrial Code
// (see end of file for more)
/* The stationary frequencies are set equal by default but can be changed, e.g. */
/* (Notice how the stop codons for this genetic code have a value of zero). */
[MODEL] M0example4
[submodel] 2.5 0.5 // kappa=2.5, w=0.5
[statefreq]
0.016133 0.014626 0.012261 0.019123 // TTT TTC TTA TTG
0.008365 0.007583 0.006357 0.009915 // TCT TCC TCA TCG
0.013290 0.012048 0 0 // TAT TAC TAA TAG
0.009947 0.009018 0 0.011790 // TGT TGC TGA TGG
0.019297 0.017494 0.014665 0.022873 // CTT CTC CTA CTG
0.010005 0.009070 0.007604 0.011859 // CCT CCC CCA CCG
0.015896 0.014410 0.012080 0.018841 // CAT CAC CAA CAG
0.011898 0.010786 0.009042 0.014102 // CGT CGC CGA CGG
0.030728 0.027857 0.023353 0.036422 // ATT ATC ATA ATG
0.015932 0.014443 0.012108 0.018884 // ACT ACC ACA ACG
0.025312 0.022947 0.019236 0.030002 // AAT AAC AAA AAG
0.018945 0.017175 0.014398 0.022456 // AGT AGC AGA AGG
0.024518 0.022227 0.018633 0.029061 // GTT GTC GTA GTG
0.012712 0.011524 0.009661 0.015068 // GCT GCC GCA GCG
0.020196 0.018309 0.015349 0.023938 // GAT GAC GAA GAG
0.015117 0.013704 0.011488 0.017919 // GGT GGC GGA GGG
/* Many different trees can be defined in a single control file */
[TREE] t1 (A:0.1,B:0.1);
[TREE] t2 ( (A:0.1, B:0.1):0.1, (C:0.3, D:0.3):0.5 );
[TREE] t3 ( species1:0.1, species2:0.1, (species3:0.2, species4:0.2):0.01 );
[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);
/* Many different partition groupings can be defined in a single control file */
[PARTITIONS] pM0_1 [t1 M0example1 20] // tree t1, model M0example1, root length 20
[PARTITIONS] pM0_2 [t2 M0example2 20] // tree t2, model M0example2, root length 20
[PARTITIONS] pM0_3 [t3 M0example3 20] // tree t3, model M0example3, root length 20
[PARTITIONS] pM0_4 [t4 M0example4 20] // tree t4, model M0example4, root length 20
/* The [EVOLVE] statement is then used to list all the simulations you want to do */
[EVOLVE]
pM0_1 5 out1 // 5 replicates generated from partition pM0_1 in file out1.fas etc
pM0_2 5 out2 // 5 replicates generated from partition pM0_2 in file out2.fas etc
pM0_3 5 out3 // 5 replicates generated from partition pM0_3 in file out3.fas etc
pM0_4 5 out4 // 5 replicates generated from partition pM0_4 in file out4.fas etc
/////////////////////////////////////////////////////////////////////////////////////
/*
Codon frequencies are changed from being equal by listing 64 numbers (separated
by white space) after the command [statefreq].
The genetic code is changed using the command [geneticcode].
e.g. [geneticcode] 3
The value should be an integer 1 to 6, 9 to 16, or 21 to 24, corresponding to the
genetic codes listed on Genbank. The value 1 (corresponding to the universal genetic
code) is the default setting if the command is not specified.
These genetic codes determine which codons are stop codons and therefore not
included in the simulation. They are also used to translate codons to amino-acids
for output if that option is chosen. The codes listed at Genbank (in Oct. 2008)
are given below (* represents a stop codon). Please note that some codes listed
are identical and only differ in terms of Starts. For more info. visit Genbank.
1 - The Standard Code
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
2 - The Vertebrate Mitochondrial Code
FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG
3 - The Yeast Mitochondrial Code
FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG
4 - The Mold, Protozoan, and Coelenterate Mitochondrial
Code and the Mycoplasma/Spiroplasma Code
FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
5 - The Invertebrate Mitochondrial Code
FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG
6 - The Ciliate, Dasycladacean and Hexamita Nuclear Code
FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
9 - The Echinoderm and Flatworm Mitochondrial Code
FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
10 - The Euplotid Nuclear Code
FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
11 - The Bacterial and Plant Plastid Code
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
12 - The Alternative Yeast Nuclear Code
FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
13 - The Ascidian Mitochondrial Code
FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG
14 - The Alternative Flatworm Mitochondrial Code
FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
15 - The Blepharisma Nuclear Code
FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
16 - The Chlorophycean Mitochondrial Code
FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
21 - The Trematode Mitochondrial Code
FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG
22 - The Scenedesmus obliquus mitochondrial Code
FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
23 - The Thraustochytrium Mitochondrial Code
FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Base1: TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2: TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3: TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
*/
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