
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:34 02/24/2011

Input data from file "/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31709.phylip" (19 taxa, 841 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
Minimum BIC  model: HKYG


Note: number of parameters compared to sample size
is low (Nchar/Nparams < 40). Consider the use of AICc.


(Output sorted by AICc. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AICc		wAICc	cwAICc
HKYG	40	-3041.1102	6166.3203	0.2668	0.2668
HKYI	40	-3041.3494	6166.7988	0.2100	0.4767
GTRG	44	-3036.9815	6166.9378	0.1959	0.6726
HKYIG	41	-3040.8014	6167.9132	0.1203	0.7929
GTRI	44	-3037.4875	6167.9499	0.1181	0.9110
GTRIG	45	-3036.6543	6168.5161	0.0890	1.0000
K2PG	37	-3068.9224	6215.3466	0.0000	1.0000
K2PI	37	-3069.2604	6216.0227	0.0000	1.0000
K2PIG	38	-3068.7462	6217.1882	0.0000	1.0000
SYMG	41	-3067.4417	6221.1937	0.0000	1.0000
SYMI	41	-3067.4549	6221.2202	0.0000	1.0000
SYMIG	42	-3066.8707	6222.2677	0.0000	1.0000
F81G	39	-3073.2275	6228.3501	0.0000	1.0000
F81I	39	-3073.5319	6228.9589	0.0000	1.0000
F81IG	40	-3073.0468	6230.1936	0.0000	1.0000
JC69G	36	-3099.6204	6274.5543	0.0000	1.0000
JC69I	36	-3099.8933	6275.1001	0.0000	1.0000
HKY	39	-3096.6764	6275.2480	0.0000	1.0000
JC69IG	37	-3099.4920	6276.4859	0.0000	1.0000
GTR	43	-3093.4714	6277.6906	0.0000	1.0000
K2P	36	-3124.8438	6325.0011	0.0000	1.0000
SYM	40	-3123.2287	6330.5574	0.0000	1.0000
F81	38	-3128.9377	6337.5712	0.0000	1.0000
JC69	35	-3155.4722	6384.0749	0.0000	1.0000



(Output sorted by AIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3036.9815	6161.9630	0.2424	0.2424
HKYG	40	-3041.1102	6162.2203	0.2132	0.4556
HKYI	40	-3041.3494	6162.6988	0.1678	0.6234
GTRI	44	-3037.4875	6162.9750	0.1462	0.7695
GTRIG	45	-3036.6543	6163.3086	0.1237	0.8932
HKYIG	41	-3040.8014	6163.6028	0.1068	1.0000
K2PG	37	-3068.9224	6211.8447	0.0000	1.0000
K2PI	37	-3069.2604	6212.5208	0.0000	1.0000
K2PIG	38	-3068.7462	6213.4924	0.0000	1.0000
SYMG	41	-3067.4417	6216.8833	0.0000	1.0000
SYMI	41	-3067.4549	6216.9098	0.0000	1.0000
SYMIG	42	-3066.8707	6217.7414	0.0000	1.0000
F81G	39	-3073.2275	6224.4550	0.0000	1.0000
F81I	39	-3073.5319	6225.0638	0.0000	1.0000
F81IG	40	-3073.0468	6226.0936	0.0000	1.0000
JC69G	36	-3099.6204	6271.2408	0.0000	1.0000
HKY	39	-3096.6764	6271.3528	0.0000	1.0000
JC69I	36	-3099.8933	6271.7867	0.0000	1.0000
GTR	43	-3093.4714	6272.9428	0.0000	1.0000
JC69IG	37	-3099.4920	6272.9840	0.0000	1.0000
K2P	36	-3124.8438	6321.6877	0.0000	1.0000
SYM	40	-3123.2287	6326.4574	0.0000	1.0000
F81	38	-3128.9377	6333.8754	0.0000	1.0000
JC69	35	-3155.4722	6380.9445	0.0000	1.0000



(Output sorted by BIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3041.1102	6351.6040	0.5452	0.5452
HKYI	40	-3041.3494	6352.0825	0.4292	0.9743
HKYIG	41	-3040.8014	6357.7211	0.0256	0.9999
GTRG	44	-3036.9815	6370.2850	0.0000	1.0000
GTRI	44	-3037.4875	6371.2970	0.0000	1.0000
GTRIG	45	-3036.6543	6376.3652	0.0000	1.0000
K2PG	37	-3068.9224	6387.0246	0.0000	1.0000
K2PI	37	-3069.2604	6387.7007	0.0000	1.0000
K2PIG	38	-3068.7462	6393.4069	0.0000	1.0000
F81G	39	-3073.2275	6409.1041	0.0000	1.0000
F81I	39	-3073.5319	6409.7129	0.0000	1.0000
SYMG	41	-3067.4417	6411.0016	0.0000	1.0000
SYMI	41	-3067.4549	6411.0281	0.0000	1.0000
F81IG	40	-3073.0468	6415.4773	0.0000	1.0000
SYMIG	42	-3066.8707	6416.5942	0.0000	1.0000
JC69G	36	-3099.6204	6441.6861	0.0000	1.0000
JC69I	36	-3099.8933	6442.2320	0.0000	1.0000
JC69IG	37	-3099.4920	6448.1639	0.0000	1.0000
HKY	39	-3096.6764	6456.0019	0.0000	1.0000
GTR	43	-3093.4714	6476.5303	0.0000	1.0000
K2P	36	-3124.8438	6492.1330	0.0000	1.0000
F81	38	-3128.9377	6513.7899	0.0000	1.0000
SYM	40	-3123.2287	6515.8410	0.0000	1.0000
JC69	35	-3155.4722	6546.6552	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31709.phylip = 1 - 841;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31709.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31709.phylip = 1 - 841;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31709.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best BIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31709.phylip = 1 - 841;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31709.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

