
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:43 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/chr2_25783.phylip" (19 taxa, 356 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	-1116.1256	2332.9844	0.5435	0.5435
GTRI	44	-1116.8294	2334.3919	0.2689	0.8123
GTRIG	45	-1115.9948	2335.3445	0.1670	0.9793
HKYG	40	-1125.3787	2341.1701	0.0091	0.9884
HKYI	40	-1125.4381	2341.2890	0.0085	0.9969
HKYIG	41	-1125.1770	2343.3221	0.0031	1.0000
GTR	43	-1131.0746	2360.2773	0.0000	1.0000
HKY	39	-1138.2377	2364.3488	0.0000	1.0000
F81I	39	-1139.1094	2366.0923	0.0000	1.0000
F81G	39	-1139.2640	2366.4014	0.0000	1.0000
F81IG	40	-1138.9789	2368.3706	0.0000	1.0000
F81	38	-1151.3194	2387.9890	0.0000	1.0000
K2PI	37	-1171.2621	2425.3669	0.0000	1.0000
K2PG	37	-1171.3559	2425.5546	0.0000	1.0000
K2PIG	38	-1171.0970	2427.5442	0.0000	1.0000
SYMI	41	-1169.4509	2431.8700	0.0000	1.0000
SYMG	41	-1169.5060	2431.9801	0.0000	1.0000
SYMIG	42	-1169.2753	2434.0906	0.0000	1.0000
JC69I	36	-1179.0424	2438.4360	0.0000	1.0000
JC69G	36	-1179.2401	2438.8314	0.0000	1.0000
JC69IG	37	-1178.9303	2440.7034	0.0000	1.0000
K2P	36	-1184.4838	2449.3187	0.0000	1.0000
SYM	40	-1182.2388	2454.8903	0.0000	1.0000
JC69	35	-1191.7409	2461.3568	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1116.1256	2320.2513	0.5191	0.5191
GTRI	44	-1116.8294	2321.6588	0.2568	0.7759
GTRIG	45	-1115.9948	2321.9897	0.2176	0.9935
HKYG	40	-1125.3787	2330.7574	0.0027	0.9962
HKYI	40	-1125.4381	2330.8763	0.0026	0.9988
HKYIG	41	-1125.1770	2332.3539	0.0012	1.0000
GTR	43	-1131.0746	2348.1491	0.0000	1.0000
HKY	39	-1138.2377	2354.4753	0.0000	1.0000
F81I	39	-1139.1094	2356.2189	0.0000	1.0000
F81G	39	-1139.2640	2356.5280	0.0000	1.0000
F81IG	40	-1138.9789	2357.9579	0.0000	1.0000
F81	38	-1151.3194	2378.6388	0.0000	1.0000
K2PI	37	-1171.2621	2416.5242	0.0000	1.0000
K2PG	37	-1171.3559	2416.7119	0.0000	1.0000
K2PIG	38	-1171.0970	2418.1940	0.0000	1.0000
SYMI	41	-1169.4509	2420.9018	0.0000	1.0000
SYMG	41	-1169.5060	2421.0120	0.0000	1.0000
SYMIG	42	-1169.2753	2422.5507	0.0000	1.0000
JC69I	36	-1179.0424	2430.0849	0.0000	1.0000
JC69G	36	-1179.2401	2430.4803	0.0000	1.0000
JC69IG	37	-1178.9303	2431.8607	0.0000	1.0000
K2P	36	-1184.4838	2440.9676	0.0000	1.0000
SYM	40	-1182.2388	2444.4776	0.0000	1.0000
JC69	35	-1191.7409	2453.4818	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1125.3787	2485.7546	0.4683	0.4683
HKYI	40	-1125.4381	2485.8735	0.4413	0.9096
GTRG	44	-1116.1256	2490.7482	0.0386	0.9482
HKYIG	41	-1125.1770	2491.2261	0.0304	0.9785
GTRI	44	-1116.8294	2492.1558	0.0191	0.9976
GTRIG	45	-1115.9948	2496.3616	0.0023	1.0000
HKY	39	-1138.2377	2505.5976	0.0000	1.0000
F81I	39	-1139.1094	2507.3412	0.0000	1.0000
F81G	39	-1139.2640	2507.6503	0.0000	1.0000
F81IG	40	-1138.9789	2512.9551	0.0000	1.0000
GTR	43	-1131.0746	2514.7712	0.0000	1.0000
F81	38	-1151.3194	2525.8862	0.0000	1.0000
K2PI	37	-1171.2621	2559.8966	0.0000	1.0000
K2PG	37	-1171.3559	2560.0843	0.0000	1.0000
K2PIG	38	-1171.0970	2565.4414	0.0000	1.0000
JC69I	36	-1179.0424	2569.5824	0.0000	1.0000
JC69G	36	-1179.2401	2569.9778	0.0000	1.0000
JC69IG	37	-1178.9303	2575.2331	0.0000	1.0000
SYMI	41	-1169.4509	2579.7740	0.0000	1.0000
SYMG	41	-1169.5060	2579.8841	0.0000	1.0000
K2P	36	-1184.4838	2580.4651	0.0000	1.0000
SYMIG	42	-1169.2753	2585.2978	0.0000	1.0000
JC69	35	-1191.7409	2589.1044	0.0000	1.0000
SYM	40	-1182.2388	2599.4748	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/chr2_25783.phylip = 1 - 356;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25783.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/chr2_25783.phylip = 1 - 356;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25783.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/chr2_25783.phylip = 1 - 356;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25783.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

