
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:10 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/chr11_1410.phylip" (19 taxa, 652 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	-2566.8283	5228.1805	0.7474	0.7474
GTRIG	45	-2566.7714	5230.3745	0.2495	0.9969
GTRI	44	-2572.4135	5239.3508	0.0028	0.9997
HKYG	40	-2579.6315	5244.6313	0.0002	0.9999
HKYIG	41	-2579.5592	5246.7642	0.0001	1.0000
HKYI	40	-2584.2398	5253.8479	0.0000	1.0000
SYMG	41	-2587.0382	5261.7223	0.0000	1.0000
SYMIG	42	-2586.9570	5263.8450	0.0000	1.0000
K2PG	37	-2594.0708	5266.7214	0.0000	1.0000
K2PIG	38	-2593.9941	5268.8234	0.0000	1.0000
SYMI	41	-2591.4221	5270.4900	0.0000	1.0000
K2PI	37	-2598.3218	5275.2233	0.0000	1.0000
GTR	43	-2606.1164	5304.4565	0.0000	1.0000
HKY	39	-2615.7099	5314.5178	0.0000	1.0000
SYM	40	-2623.4458	5332.2598	0.0000	1.0000
K2P	36	-2629.2926	5334.9168	0.0000	1.0000
F81G	39	-2636.0106	5355.1192	0.0000	1.0000
F81IG	40	-2635.9836	5357.3354	0.0000	1.0000
F81I	39	-2640.4034	5363.9049	0.0000	1.0000
JC69G	36	-2646.2447	5368.8211	0.0000	1.0000
JC69IG	37	-2646.2124	5371.0045	0.0000	1.0000
JC69I	36	-2650.5016	5377.3349	0.0000	1.0000
F81	38	-2669.7614	5420.3580	0.0000	1.0000
JC69	35	-2679.8459	5433.7827	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2566.8283	5221.6567	0.7177	0.7177
GTRIG	45	-2566.7714	5223.5428	0.2795	0.9972
GTRI	44	-2572.4135	5232.8269	0.0027	0.9998
HKYG	40	-2579.6315	5239.2630	0.0001	1.0000
HKYIG	41	-2579.5592	5241.1183	0.0000	1.0000
HKYI	40	-2584.2398	5248.4796	0.0000	1.0000
SYMG	41	-2587.0382	5256.0764	0.0000	1.0000
SYMIG	42	-2586.9570	5257.9140	0.0000	1.0000
K2PG	37	-2594.0708	5262.1416	0.0000	1.0000
K2PIG	38	-2593.9941	5263.9881	0.0000	1.0000
SYMI	41	-2591.4221	5264.8441	0.0000	1.0000
K2PI	37	-2598.3218	5270.6435	0.0000	1.0000
GTR	43	-2606.1164	5298.2328	0.0000	1.0000
HKY	39	-2615.7099	5309.4198	0.0000	1.0000
SYM	40	-2623.4458	5326.8915	0.0000	1.0000
K2P	36	-2629.2926	5330.5851	0.0000	1.0000
F81G	39	-2636.0106	5350.0212	0.0000	1.0000
F81IG	40	-2635.9836	5351.9672	0.0000	1.0000
F81I	39	-2640.4034	5358.8069	0.0000	1.0000
JC69G	36	-2646.2447	5364.4894	0.0000	1.0000
JC69IG	37	-2646.2124	5366.4247	0.0000	1.0000
JC69I	36	-2650.5016	5373.0032	0.0000	1.0000
F81	38	-2669.7614	5415.5227	0.0000	1.0000
JC69	35	-2679.8459	5429.6918	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2579.6315	5418.4648	0.5115	0.5115
GTRG	44	-2566.8283	5418.7786	0.4372	0.9488
HKYIG	41	-2579.5592	5424.8001	0.0215	0.9703
GTRIG	45	-2566.7714	5425.1448	0.0181	0.9884
HKYI	40	-2584.2398	5427.6814	0.0051	0.9935
K2PG	37	-2594.0708	5427.9032	0.0046	0.9981
GTRI	44	-2572.4135	5429.9489	0.0016	0.9997
K2PIG	38	-2593.9941	5434.2298	0.0002	0.9999
K2PI	37	-2598.3218	5436.4052	0.0001	1.0000
SYMG	41	-2587.0382	5439.7582	0.0000	1.0000
SYMIG	42	-2586.9570	5446.0759	0.0000	1.0000
SYMI	41	-2591.4221	5448.5259	0.0000	1.0000
HKY	39	-2615.7099	5484.1415	0.0000	1.0000
GTR	43	-2606.1164	5490.8747	0.0000	1.0000
K2P	36	-2629.2926	5491.8667	0.0000	1.0000
SYM	40	-2623.4458	5506.0933	0.0000	1.0000
F81G	39	-2636.0106	5524.7429	0.0000	1.0000
JC69G	36	-2646.2447	5525.7710	0.0000	1.0000
F81IG	40	-2635.9836	5531.1690	0.0000	1.0000
JC69IG	37	-2646.2124	5532.1864	0.0000	1.0000
F81I	39	-2640.4034	5533.5286	0.0000	1.0000
JC69I	36	-2650.5016	5534.2848	0.0000	1.0000
F81	38	-2669.7614	5585.7644	0.0000	1.0000
JC69	35	-2679.8459	5586.4933	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/chr11_1410.phylip = 1 - 652;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1410.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/chr11_1410.phylip = 1 - 652;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1410.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/chr11_1410.phylip = 1 - 652;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1410.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;


-------------------------------------------------------------
End of Output

