
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:44 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/chr7_11510.phylip" (19 taxa, 719 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-2595.7251	5285.3256	0.7390	0.7390
GTRIG	45	-2595.6751	5287.5017	0.2489	0.9879
GTRI	44	-2600.3677	5294.6107	0.0071	0.9950
HKYG	40	-2606.4025	5297.6428	0.0016	0.9966
SYMG	41	-2605.4590	5298.0051	0.0013	0.9979
SYMIG	42	-2604.8537	5299.0505	0.0008	0.9987
HKYIG	41	-2606.3704	5299.8279	0.0005	0.9992
K2PG	37	-2611.2301	5300.5894	0.0004	0.9995
HKYI	40	-2608.6118	5302.0614	0.0002	0.9997
K2PIG	38	-2611.1934	5302.7455	0.0001	0.9998
SYMI	41	-2607.9009	5302.8889	0.0001	1.0000
K2PI	37	-2613.2773	5304.6839	0.0000	1.0000
GTR	43	-2626.9482	5345.5022	0.0000	1.0000
HKY	39	-2635.2931	5353.1813	0.0000	1.0000
SYM	40	-2634.4916	5353.8209	0.0000	1.0000
K2P	36	-2639.7946	5355.4954	0.0000	1.0000
F81G	39	-2659.2789	5401.1529	0.0000	1.0000
F81IG	40	-2659.2647	5403.3671	0.0000	1.0000
JC69G	36	-2663.8720	5403.6502	0.0000	1.0000
JC69IG	37	-2663.0284	5404.1861	0.0000	1.0000
F81I	39	-2661.3317	5405.2583	0.0000	1.0000
JC69I	36	-2665.0526	5406.0114	0.0000	1.0000
F81	38	-2684.6911	5449.7411	0.0000	1.0000
JC69	35	-2688.2454	5450.1803	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2595.7251	5279.4502	0.7139	0.7139
GTRIG	45	-2595.6751	5281.3501	0.2761	0.9901
GTRI	44	-2600.3677	5288.7354	0.0069	0.9969
HKYG	40	-2606.4025	5292.8051	0.0009	0.9978
SYMG	41	-2605.4590	5292.9179	0.0008	0.9987
SYMIG	42	-2604.8537	5293.7073	0.0006	0.9993
HKYIG	41	-2606.3704	5294.7407	0.0003	0.9996
K2PG	37	-2611.2301	5296.4602	0.0001	0.9998
HKYI	40	-2608.6118	5297.2237	0.0001	0.9999
SYMI	41	-2607.9009	5297.8017	0.0001	0.9999
K2PIG	38	-2611.1934	5298.3867	0.0001	1.0000
K2PI	37	-2613.2773	5300.5547	0.0000	1.0000
GTR	43	-2626.9482	5339.8963	0.0000	1.0000
HKY	39	-2635.2931	5348.5863	0.0000	1.0000
SYM	40	-2634.4916	5348.9832	0.0000	1.0000
K2P	36	-2639.7946	5351.5892	0.0000	1.0000
F81G	39	-2659.2789	5396.5579	0.0000	1.0000
F81IG	40	-2659.2647	5398.5294	0.0000	1.0000
JC69G	36	-2663.8720	5399.7440	0.0000	1.0000
JC69IG	37	-2663.0284	5400.0568	0.0000	1.0000
F81I	39	-2661.3317	5400.6633	0.0000	1.0000
JC69I	36	-2665.0526	5402.1052	0.0000	1.0000
F81	38	-2684.6911	5445.3823	0.0000	1.0000
JC69	35	-2688.2454	5446.4907	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2611.2301	5465.8411	0.8500	0.8500
K2PI	37	-2613.2773	5469.9356	0.1097	0.9597
K2PIG	38	-2611.1934	5472.3455	0.0329	0.9926
HKYG	40	-2606.4025	5475.9195	0.0055	0.9981
HKYI	40	-2608.6118	5480.3381	0.0006	0.9987
SYMG	41	-2605.4590	5480.6102	0.0005	0.9992
GTRG	44	-2595.7251	5480.8761	0.0005	0.9997
HKYIG	41	-2606.3704	5482.4331	0.0002	0.9999
SYMI	41	-2607.9009	5485.4941	0.0000	0.9999
SYMIG	42	-2604.8537	5485.9775	0.0000	1.0000
GTRIG	45	-2595.6751	5487.3539	0.0000	1.0000
GTRI	44	-2600.3677	5490.1613	0.0000	1.0000
K2P	36	-2639.7946	5516.3922	0.0000	1.0000
HKY	39	-2635.2931	5527.1229	0.0000	1.0000
SYM	40	-2634.4916	5532.0976	0.0000	1.0000
GTR	43	-2626.9482	5536.7444	0.0000	1.0000
JC69G	36	-2663.8720	5564.5470	0.0000	1.0000
JC69I	36	-2665.0526	5566.9082	0.0000	1.0000
JC69IG	37	-2663.0284	5569.4377	0.0000	1.0000
F81G	39	-2659.2789	5575.0945	0.0000	1.0000
F81I	39	-2661.3317	5579.1999	0.0000	1.0000
F81IG	40	-2659.2647	5581.6438	0.0000	1.0000
JC69	35	-2688.2454	5606.7159	0.0000	1.0000
F81	38	-2684.6911	5619.3410	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/chr7_11510.phylip = 1 - 719;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11510.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/chr7_11510.phylip = 1 - 719;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11510.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11510.phylip = 1 - 719;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11510.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

