
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:09 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_3556.phylip" (19 taxa, 601 characters)

Minimum AIC  model: SYMG
Minimum AICc model: SYMG
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
SYMG	41	-2537.5916	5163.3443	0.4918	0.4918
GTRG	44	-2534.8899	5164.9021	0.2257	0.7175
SYMIG	42	-2537.3889	5165.2508	0.1896	0.9071
GTRIG	45	-2534.7000	5166.8594	0.0848	0.9919
K2PG	37	-2546.5238	5172.0423	0.0064	0.9982
K2PIG	38	-2546.8936	5175.0612	0.0014	0.9996
HKYG	40	-2546.1658	5178.1887	0.0003	0.9999
HKYIG	41	-2546.4967	5181.1543	0.0001	1.0000
SYMI	41	-2549.3723	5186.9056	0.0000	1.0000
GTRI	44	-2548.2499	5191.6221	0.0000	1.0000
K2PI	37	-2558.2854	5195.5656	0.0000	1.0000
HKYI	40	-2558.9405	5203.7381	0.0000	1.0000
SYM	40	-2584.7445	5255.3462	0.0000	1.0000
GTR	43	-2582.2829	5257.3594	0.0000	1.0000
K2P	36	-2593.1409	5263.0052	0.0000	1.0000
JC69G	36	-2595.5405	5267.8044	0.0000	1.0000
HKY	39	-2592.5619	5268.6854	0.0000	1.0000
JC69IG	37	-2595.3566	5269.7079	0.0000	1.0000
F81G	39	-2595.2256	5274.0128	0.0000	1.0000
F81IG	40	-2595.0452	5275.9476	0.0000	1.0000
JC69I	36	-2606.5554	5289.8341	0.0000	1.0000
F81I	39	-2606.2631	5296.0876	0.0000	1.0000
JC69	35	-2639.1212	5352.7025	0.0000	1.0000
F81	38	-2638.8184	5358.9108	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
SYMG	41	-2537.5916	5157.1833	0.3949	0.3949
GTRG	44	-2534.8899	5157.7798	0.2930	0.6879
SYMIG	42	-2537.3889	5158.7777	0.1779	0.8658
GTRIG	45	-2534.7000	5159.3999	0.1304	0.9962
K2PG	37	-2546.5238	5167.0476	0.0028	0.9990
K2PIG	38	-2546.8936	5169.7872	0.0007	0.9997
HKYG	40	-2546.1658	5172.3316	0.0002	0.9999
HKYIG	41	-2546.4967	5174.9933	0.0001	1.0000
SYMI	41	-2549.3723	5180.7446	0.0000	1.0000
GTRI	44	-2548.2499	5184.4998	0.0000	1.0000
K2PI	37	-2558.2854	5190.5709	0.0000	1.0000
HKYI	40	-2558.9405	5197.8809	0.0000	1.0000
SYM	40	-2584.7445	5249.4890	0.0000	1.0000
GTR	43	-2582.2829	5250.5659	0.0000	1.0000
K2P	36	-2593.1409	5258.2818	0.0000	1.0000
JC69G	36	-2595.5405	5263.0810	0.0000	1.0000
HKY	39	-2592.5619	5263.1239	0.0000	1.0000
JC69IG	37	-2595.3566	5264.7132	0.0000	1.0000
F81G	39	-2595.2256	5268.4513	0.0000	1.0000
F81IG	40	-2595.0452	5270.0905	0.0000	1.0000
JC69I	36	-2606.5554	5285.1107	0.0000	1.0000
F81I	39	-2606.2631	5290.5261	0.0000	1.0000
JC69	35	-2639.1212	5348.2423	0.0000	1.0000
F81	38	-2638.8184	5353.6368	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2546.5238	5329.7956	0.9521	0.9521
K2PIG	38	-2546.8936	5336.9338	0.0268	0.9789
SYMG	41	-2537.5916	5337.5257	0.0200	0.9989
SYMIG	42	-2537.3889	5343.5187	0.0010	0.9999
HKYG	40	-2546.1658	5348.2754	0.0001	1.0000
GTRG	44	-2534.8899	5351.3180	0.0000	1.0000
K2PI	37	-2558.2854	5353.3189	0.0000	1.0000
HKYIG	41	-2546.4967	5355.3357	0.0000	1.0000
GTRIG	45	-2534.7000	5357.3367	0.0000	1.0000
SYMI	41	-2549.3723	5361.0870	0.0000	1.0000
HKYI	40	-2558.9405	5373.8247	0.0000	1.0000
GTRI	44	-2548.2499	5378.0380	0.0000	1.0000
K2P	36	-2593.1409	5416.6312	0.0000	1.0000
JC69G	36	-2595.5405	5421.4304	0.0000	1.0000
SYM	40	-2584.7445	5425.4328	0.0000	1.0000
JC69IG	37	-2595.3566	5427.4612	0.0000	1.0000
HKY	39	-2592.5619	5434.6691	0.0000	1.0000
GTR	43	-2582.2829	5439.7054	0.0000	1.0000
F81G	39	-2595.2256	5439.9965	0.0000	1.0000
JC69I	36	-2606.5554	5443.4601	0.0000	1.0000
F81IG	40	-2595.0452	5446.0343	0.0000	1.0000
F81I	39	-2606.2631	5462.0713	0.0000	1.0000
JC69	35	-2639.1212	5502.1932	0.0000	1.0000
F81	38	-2638.8184	5520.7834	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3556.phylip = 1 - 601;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3556.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=Fixed(Equal);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3556.phylip = 1 - 601;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3556.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=Fixed(Equal);
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/chr11_3556.phylip = 1 - 601;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3556.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;


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

