
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:24 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/chr17_2991.phylip" (19 taxa, 693 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	-2665.9552	5426.0215	0.7337	0.7337
GTRIG	45	-2665.9562	5428.3112	0.2335	0.9672
HKYG	40	-2674.1649	5433.3605	0.0187	0.9859
GTRI	44	-2670.4916	5435.0944	0.0079	0.9937
HKYIG	41	-2674.1643	5435.6189	0.0060	0.9998
HKYI	40	-2678.5563	5442.1433	0.0002	1.0000
SYMG	41	-2695.1198	5477.5300	0.0000	1.0000
K2PG	37	-2700.4337	5479.1606	0.0000	1.0000
SYMIG	42	-2695.0884	5479.7338	0.0000	1.0000
K2PIG	38	-2700.4013	5481.3346	0.0000	1.0000
SYMI	41	-2698.9855	5485.2612	0.0000	1.0000
GTR	43	-2697.7790	5487.3885	0.0000	1.0000
K2PI	37	-2704.7053	5487.7037	0.0000	1.0000
HKY	39	-2705.5635	5493.9049	0.0000	1.0000
SYM	40	-2726.7261	5538.4829	0.0000	1.0000
K2P	36	-2732.9721	5542.0051	0.0000	1.0000
F81G	39	-2749.3020	5581.3820	0.0000	1.0000
F81IG	40	-2749.2907	5583.6120	0.0000	1.0000
F81I	39	-2753.3369	5589.4518	0.0000	1.0000
JC69G	36	-2770.1249	5616.3107	0.0000	1.0000
JC69IG	37	-2770.0989	5618.4909	0.0000	1.0000
JC69I	36	-2774.0323	5624.1257	0.0000	1.0000
F81	38	-2778.8880	5638.3080	0.0000	1.0000
JC69	35	-2800.1849	5674.2055	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2665.9552	5419.9104	0.7149	0.7149
GTRIG	45	-2665.9562	5421.9124	0.2627	0.9777
HKYG	40	-2674.1649	5428.3298	0.0106	0.9883
GTRI	44	-2670.4916	5428.9832	0.0077	0.9960
HKYIG	41	-2674.1643	5430.3286	0.0039	0.9999
HKYI	40	-2678.5563	5437.1126	0.0001	1.0000
SYMG	41	-2695.1198	5472.2396	0.0000	1.0000
SYMIG	42	-2695.0884	5474.1768	0.0000	1.0000
K2PG	37	-2700.4337	5474.8675	0.0000	1.0000
K2PIG	38	-2700.4013	5476.8025	0.0000	1.0000
SYMI	41	-2698.9855	5479.9709	0.0000	1.0000
GTR	43	-2697.7790	5481.5580	0.0000	1.0000
K2PI	37	-2704.7053	5483.4106	0.0000	1.0000
HKY	39	-2705.5635	5489.1269	0.0000	1.0000
SYM	40	-2726.7261	5533.4522	0.0000	1.0000
K2P	36	-2732.9721	5537.9442	0.0000	1.0000
F81G	39	-2749.3020	5576.6040	0.0000	1.0000
F81IG	40	-2749.2907	5578.5813	0.0000	1.0000
F81I	39	-2753.3369	5584.6739	0.0000	1.0000
JC69G	36	-2770.1249	5612.2497	0.0000	1.0000
JC69IG	37	-2770.0989	5614.1977	0.0000	1.0000
JC69I	36	-2774.0323	5620.0647	0.0000	1.0000
F81	38	-2778.8880	5633.7759	0.0000	1.0000
JC69	35	-2800.1849	5670.3699	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2674.1649	5609.9710	0.9448	0.9448
HKYIG	41	-2674.1643	5616.5108	0.0359	0.9807
HKYI	40	-2678.5563	5618.7538	0.0117	0.9924
GTRG	44	-2665.9552	5619.7157	0.0072	0.9996
GTRIG	45	-2665.9562	5626.2588	0.0003	0.9999
GTRI	44	-2670.4916	5628.7886	0.0001	1.0000
K2PG	37	-2700.4337	5642.8856	0.0000	1.0000
K2PIG	38	-2700.4013	5649.3617	0.0000	1.0000
K2PI	37	-2704.7053	5651.4287	0.0000	1.0000
SYMG	41	-2695.1198	5658.4219	0.0000	1.0000
SYMIG	42	-2695.0884	5664.9001	0.0000	1.0000
SYMI	41	-2698.9855	5666.1531	0.0000	1.0000
HKY	39	-2705.5635	5666.2271	0.0000	1.0000
GTR	43	-2697.7790	5676.8223	0.0000	1.0000
K2P	36	-2732.9721	5701.4212	0.0000	1.0000
SYM	40	-2726.7261	5715.0934	0.0000	1.0000
F81G	39	-2749.3020	5753.7042	0.0000	1.0000
F81IG	40	-2749.2907	5760.2225	0.0000	1.0000
F81I	39	-2753.3369	5761.7740	0.0000	1.0000
JC69G	36	-2770.1249	5775.7268	0.0000	1.0000
JC69IG	37	-2770.0989	5782.2158	0.0000	1.0000
JC69I	36	-2774.0323	5783.5418	0.0000	1.0000
F81	38	-2778.8880	5806.3351	0.0000	1.0000
JC69	35	-2800.1849	5829.3059	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/chr17_2991.phylip = 1 - 693;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_2991.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/chr17_2991.phylip = 1 - 693;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_2991.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/chr17_2991.phylip = 1 - 693;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_2991.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

