
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:40 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/chr12_5999.phylip" (19 taxa, 752 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-2616.3231	5328.5102	0.7226	0.7226
GTRG	44	-2618.7599	5331.1209	0.1959	0.9185
HKYIG	41	-2623.2553	5333.3614	0.0639	0.9824
HKYG	40	-2625.6897	5335.9927	0.0171	0.9996
GTRI	44	-2625.1304	5343.8619	0.0003	0.9999
HKYI	40	-2631.0833	5346.7798	0.0001	1.0000
K2PIG	38	-2654.9213	5389.9997	0.0000	1.0000
K2PG	37	-2657.9723	5393.8831	0.0000	1.0000
SYMIG	42	-2653.0369	5395.1684	0.0000	1.0000
SYMG	41	-2655.1136	5397.0779	0.0000	1.0000
K2PI	37	-2663.1566	5404.2517	0.0000	1.0000
SYMI	41	-2660.8534	5408.5575	0.0000	1.0000
F81IG	40	-2684.5872	5453.7875	0.0000	1.0000
F81G	39	-2687.1716	5456.7251	0.0000	1.0000
F81I	39	-2692.9095	5468.2010	0.0000	1.0000
JC69IG	37	-2711.8268	5501.5920	0.0000	1.0000
JC69G	36	-2714.1110	5503.9478	0.0000	1.0000
JC69I	36	-2719.4003	5514.5265	0.0000	1.0000
GTR	43	-2712.0569	5515.4584	0.0000	1.0000
HKY	39	-2718.7619	5519.9058	0.0000	1.0000
K2P	36	-2753.3945	5582.5148	0.0000	1.0000
SYM	40	-2750.9889	5586.5910	0.0000	1.0000
F81	38	-2778.4766	5637.1103	0.0000	1.0000
JC69	35	-2806.2101	5685.9398	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2616.3231	5322.6462	0.7668	0.7668
GTRG	44	-2618.7599	5325.5197	0.1823	0.9491
HKYIG	41	-2623.2553	5328.5107	0.0409	0.9899
HKYG	40	-2625.6897	5331.3795	0.0097	0.9996
GTRI	44	-2625.1304	5338.2608	0.0003	1.0000
HKYI	40	-2631.0833	5342.1666	0.0000	1.0000
K2PIG	38	-2654.9213	5385.8427	0.0000	1.0000
K2PG	37	-2657.9723	5389.9447	0.0000	1.0000
SYMIG	42	-2653.0369	5390.0739	0.0000	1.0000
SYMG	41	-2655.1136	5392.2272	0.0000	1.0000
K2PI	37	-2663.1566	5400.3133	0.0000	1.0000
SYMI	41	-2660.8534	5403.7068	0.0000	1.0000
F81IG	40	-2684.5872	5449.1743	0.0000	1.0000
F81G	39	-2687.1716	5452.3431	0.0000	1.0000
F81I	39	-2692.9095	5463.8190	0.0000	1.0000
JC69IG	37	-2711.8268	5497.6536	0.0000	1.0000
JC69G	36	-2714.1110	5500.2219	0.0000	1.0000
GTR	43	-2712.0569	5510.1138	0.0000	1.0000
JC69I	36	-2719.4003	5510.8006	0.0000	1.0000
HKY	39	-2718.7619	5515.5238	0.0000	1.0000
K2P	36	-2753.3945	5578.7889	0.0000	1.0000
SYM	40	-2750.9889	5581.9778	0.0000	1.0000
F81	38	-2778.4766	5632.9533	0.0000	1.0000
JC69	35	-2806.2101	5682.4202	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2625.6897	5516.2889	0.7027	0.7027
HKYIG	41	-2623.2553	5518.0428	0.2923	0.9950
HKYI	40	-2631.0833	5527.0761	0.0032	0.9982
GTRG	44	-2618.7599	5528.9201	0.0013	0.9995
GTRIG	45	-2616.3231	5530.6693	0.0005	1.0000
GTRI	44	-2625.1304	5541.6612	0.0000	1.0000
K2PG	37	-2657.9723	5560.9859	0.0000	1.0000
K2PIG	38	-2654.9213	5561.5066	0.0000	1.0000
K2PI	37	-2663.1566	5571.3545	0.0000	1.0000
SYMG	41	-2655.1136	5581.7594	0.0000	1.0000
SYMIG	42	-2653.0369	5584.2288	0.0000	1.0000
SYMI	41	-2660.8534	5593.2390	0.0000	1.0000
F81G	39	-2687.1716	5632.6298	0.0000	1.0000
F81IG	40	-2684.5872	5634.0838	0.0000	1.0000
F81I	39	-2692.9095	5644.1057	0.0000	1.0000
JC69G	36	-2714.1110	5666.6404	0.0000	1.0000
JC69IG	37	-2711.8268	5668.6949	0.0000	1.0000
JC69I	36	-2719.4003	5677.2191	0.0000	1.0000
HKY	39	-2718.7619	5695.8105	0.0000	1.0000
GTR	43	-2712.0569	5708.8914	0.0000	1.0000
K2P	36	-2753.3945	5745.2074	0.0000	1.0000
SYM	40	-2750.9889	5766.8872	0.0000	1.0000
F81	38	-2778.4766	5808.6172	0.0000	1.0000
JC69	35	-2806.2101	5844.2160	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5999.phylip = 1 - 752;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5999.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5999.phylip = 1 - 752;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5999.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr12_5999.phylip = 1 - 752;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5999.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

