
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:33 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_5923.phylip" (19 taxa, 436 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	-1177.5214	2453.1707	0.5005	0.5005
GTRI	44	-1177.9187	2453.9654	0.3364	0.8369
GTRIG	45	-1177.4752	2455.5658	0.1511	0.9880
HKYG	40	-1186.9059	2462.1156	0.0057	0.9937
HKYI	40	-1187.1744	2462.6525	0.0044	0.9981
HKYIG	41	-1186.8638	2464.4688	0.0018	0.9998
GTR	43	-1186.7685	2469.1901	0.0002	1.0000
HKY	39	-1195.9662	2477.8112	0.0000	1.0000
F81G	39	-1201.2259	2488.3306	0.0000	1.0000
F81I	39	-1201.4039	2488.6866	0.0000	1.0000
F81IG	40	-1201.1846	2490.6730	0.0000	1.0000
K2PG	37	-1210.3963	2501.8580	0.0000	1.0000
K2PI	37	-1210.6080	2502.2812	0.0000	1.0000
SYMG	41	-1206.5035	2503.7481	0.0000	1.0000
F81	38	-1210.2075	2503.8809	0.0000	1.0000
K2PIG	38	-1210.3504	2504.1668	0.0000	1.0000
SYMI	41	-1206.7231	2504.1873	0.0000	1.0000
SYMIG	42	-1206.4672	2506.1252	0.0000	1.0000
K2P	36	-1220.0884	2518.8535	0.0000	1.0000
SYM	40	-1215.5727	2519.4492	0.0000	1.0000
JC69G	36	-1222.6451	2523.9669	0.0000	1.0000
JC69I	36	-1222.8050	2524.2868	0.0000	1.0000
JC69IG	37	-1222.6111	2526.2875	0.0000	1.0000
JC69	35	-1232.0943	2540.4886	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1177.5214	2443.0428	0.4837	0.4837
GTRI	44	-1177.9187	2443.8375	0.3251	0.8088
GTRIG	45	-1177.4752	2444.9504	0.1863	0.9951
HKYG	40	-1186.9059	2453.8118	0.0022	0.9973
HKYI	40	-1187.1744	2454.3487	0.0017	0.9990
HKYIG	41	-1186.8638	2455.7277	0.0009	0.9999
GTR	43	-1186.7685	2459.5370	0.0001	1.0000
HKY	39	-1195.9662	2469.9325	0.0000	1.0000
F81G	39	-1201.2259	2480.4518	0.0000	1.0000
F81I	39	-1201.4039	2480.8078	0.0000	1.0000
F81IG	40	-1201.1846	2482.3692	0.0000	1.0000
K2PG	37	-1210.3963	2494.7927	0.0000	1.0000
SYMG	41	-1206.5035	2495.0070	0.0000	1.0000
K2PI	37	-1210.6080	2495.2159	0.0000	1.0000
SYMI	41	-1206.7231	2495.4462	0.0000	1.0000
F81	38	-1210.2075	2496.4149	0.0000	1.0000
K2PIG	38	-1210.3504	2496.7008	0.0000	1.0000
SYMIG	42	-1206.4672	2496.9343	0.0000	1.0000
SYM	40	-1215.5727	2511.1454	0.0000	1.0000
K2P	36	-1220.0884	2512.1768	0.0000	1.0000
JC69G	36	-1222.6451	2517.2902	0.0000	1.0000
JC69I	36	-1222.8050	2517.6101	0.0000	1.0000
JC69IG	37	-1222.6111	2519.2222	0.0000	1.0000
JC69	35	-1232.0943	2534.1886	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1186.9059	2616.9175	0.5195	0.5195
HKYI	40	-1187.1744	2617.4544	0.3972	0.9167
GTRG	44	-1177.5214	2622.4591	0.0325	0.9492
HKYIG	41	-1186.8638	2622.9110	0.0259	0.9752
GTRI	44	-1177.9187	2623.2537	0.0219	0.9970
GTRIG	45	-1177.4752	2628.4443	0.0016	0.9987
HKY	39	-1195.9662	2628.9605	0.0013	0.9999
GTR	43	-1186.7685	2634.8757	0.0001	1.0000
F81G	39	-1201.2259	2639.4799	0.0000	1.0000
F81I	39	-1201.4039	2639.8359	0.0000	1.0000
F81IG	40	-1201.1846	2645.4748	0.0000	1.0000
K2PG	37	-1210.3963	2645.6655	0.0000	1.0000
K2PI	37	-1210.6080	2646.0887	0.0000	1.0000
F81	38	-1210.2075	2651.3653	0.0000	1.0000
K2PIG	38	-1210.3504	2651.6512	0.0000	1.0000
K2P	36	-1220.0884	2658.9719	0.0000	1.0000
SYMG	41	-1206.5035	2662.1904	0.0000	1.0000
SYMI	41	-1206.7231	2662.6295	0.0000	1.0000
JC69G	36	-1222.6451	2664.0853	0.0000	1.0000
JC69I	36	-1222.8050	2664.4052	0.0000	1.0000
SYMIG	42	-1206.4672	2668.1953	0.0000	1.0000
JC69IG	37	-1222.6111	2670.0949	0.0000	1.0000
SYM	40	-1215.5727	2674.2510	0.0000	1.0000
JC69	35	-1232.0943	2676.9061	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/chr12_5923.phylip = 1 - 436;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5923.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/chr12_5923.phylip = 1 - 436;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5923.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/chr12_5923.phylip = 1 - 436;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5923.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

