
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:02 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/chr9_5281.phylip" (19 taxa, 823 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-2231.1661	4555.4222	0.4418	0.4418
GTRI	44	-2231.2966	4555.6833	0.3877	0.8295
GTRIG	45	-2231.0316	4557.3914	0.1650	0.9945
HKYG	40	-2240.8418	4565.8780	0.0024	0.9969
HKYI	40	-2240.8601	4565.9146	0.0023	0.9992
HKYIG	41	-2240.8411	4568.0919	0.0008	1.0000
F81G	39	-2265.2684	4612.5215	0.0000	1.0000
F81I	39	-2265.3017	4612.5882	0.0000	1.0000
F81IG	40	-2265.2591	4614.7125	0.0000	1.0000
SYMI	41	-2269.5279	4625.4656	0.0000	1.0000
SYMG	41	-2269.5871	4625.5839	0.0000	1.0000
SYMIG	42	-2269.5872	4627.8052	0.0000	1.0000
K2PI	37	-2275.1833	4627.9487	0.0000	1.0000
K2PG	37	-2275.2015	4627.9851	0.0000	1.0000
K2PIG	38	-2275.2015	4630.1836	0.0000	1.0000
GTR	43	-2284.6308	4660.1192	0.0000	1.0000
HKY	39	-2293.0242	4668.0331	0.0000	1.0000
JC69I	36	-2296.7718	4668.9328	0.0000	1.0000
JC69G	36	-2296.7863	4668.9618	0.0000	1.0000
JC69IG	37	-2296.7862	4671.1546	0.0000	1.0000
F81	38	-2316.2673	4712.3153	0.0000	1.0000
SYM	40	-2322.9635	4730.1213	0.0000	1.0000
K2P	36	-2327.8397	4731.0687	0.0000	1.0000
JC69	35	-2348.1818	4769.5656	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2231.1661	4550.3323	0.4335	0.4335
GTRI	44	-2231.2966	4550.5933	0.3805	0.8140
GTRIG	45	-2231.0316	4552.0632	0.1825	0.9965
HKYG	40	-2240.8418	4561.6836	0.0015	0.9980
HKYI	40	-2240.8601	4561.7202	0.0015	0.9995
HKYIG	41	-2240.8411	4563.6821	0.0005	1.0000
F81G	39	-2265.2684	4608.5368	0.0000	1.0000
F81I	39	-2265.3017	4608.6035	0.0000	1.0000
F81IG	40	-2265.2591	4610.5181	0.0000	1.0000
SYMI	41	-2269.5279	4621.0558	0.0000	1.0000
SYMG	41	-2269.5871	4621.1741	0.0000	1.0000
SYMIG	42	-2269.5872	4623.1744	0.0000	1.0000
K2PI	37	-2275.1833	4624.3665	0.0000	1.0000
K2PG	37	-2275.2015	4624.4029	0.0000	1.0000
K2PIG	38	-2275.2015	4626.4029	0.0000	1.0000
GTR	43	-2284.6308	4655.2617	0.0000	1.0000
HKY	39	-2293.0242	4664.0484	0.0000	1.0000
JC69I	36	-2296.7718	4665.5435	0.0000	1.0000
JC69G	36	-2296.7863	4665.5725	0.0000	1.0000
JC69IG	37	-2296.7862	4667.5724	0.0000	1.0000
F81	38	-2316.2673	4708.5346	0.0000	1.0000
SYM	40	-2322.9635	4725.9269	0.0000	1.0000
K2P	36	-2327.8397	4727.6794	0.0000	1.0000
JC69	35	-2348.1818	4766.3635	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2240.8418	4750.2019	0.4850	0.4850
HKYI	40	-2240.8601	4750.2385	0.4762	0.9612
HKYIG	41	-2240.8411	4756.9133	0.0169	0.9781
GTRG	44	-2231.1661	4757.7023	0.0114	0.9895
GTRI	44	-2231.2966	4757.9634	0.0100	0.9995
GTRIG	45	-2231.0316	4764.1462	0.0005	1.0000
F81G	39	-2265.2684	4792.3421	0.0000	1.0000
F81I	39	-2265.3017	4792.4088	0.0000	1.0000
K2PI	37	-2275.1833	4798.7459	0.0000	1.0000
K2PG	37	-2275.2015	4798.7823	0.0000	1.0000
F81IG	40	-2265.2591	4799.0364	0.0000	1.0000
K2PIG	38	-2275.2015	4805.4953	0.0000	1.0000
SYMI	41	-2269.5279	4814.2870	0.0000	1.0000
SYMG	41	-2269.5871	4814.4053	0.0000	1.0000
SYMIG	42	-2269.5872	4821.1186	0.0000	1.0000
JC69I	36	-2296.7718	4835.2099	0.0000	1.0000
JC69G	36	-2296.7863	4835.2389	0.0000	1.0000
JC69IG	37	-2296.7862	4841.9518	0.0000	1.0000
HKY	39	-2293.0242	4847.8537	0.0000	1.0000
GTR	43	-2284.6308	4857.9188	0.0000	1.0000
F81	38	-2316.2673	4887.6270	0.0000	1.0000
K2P	36	-2327.8397	4897.3458	0.0000	1.0000
SYM	40	-2322.9635	4914.4451	0.0000	1.0000
JC69	35	-2348.1818	4931.3170	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/chr9_5281.phylip = 1 - 823;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5281.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5281.phylip = 1 - 823;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5281.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 BIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5281.phylip = 1 - 823;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5281.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

