
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:46 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/chr3_25095.phylip" (19 taxa, 511 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: HKYI


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
HKYI	40	-1377.0697	2841.1182	0.3939	0.3939
HKYG	40	-1377.3158	2841.6102	0.3080	0.7019
GTRI	44	-1373.7280	2843.9538	0.0954	0.7973
HKYIG	41	-1377.3155	2843.9743	0.0945	0.8918
GTRG	44	-1373.8650	2844.2278	0.0832	0.9750
GTRIG	45	-1373.8647	2846.6327	0.0250	1.0000
K2PI	37	-1401.8509	2883.6469	0.0000	1.0000
K2PG	37	-1402.0173	2883.9797	0.0000	1.0000
K2PIG	38	-1402.0170	2886.3138	0.0000	1.0000
SYMG	41	-1400.7354	2890.8141	0.0000	1.0000
SYMI	41	-1400.8845	2891.1122	0.0000	1.0000
GTR	43	-1399.3344	2892.7715	0.0000	1.0000
SYMIG	42	-1400.7361	2893.1902	0.0000	1.0000
HKY	39	-1404.5218	2893.6678	0.0000	1.0000
F81I	39	-1414.0456	2912.7154	0.0000	1.0000
F81G	39	-1414.2217	2913.0676	0.0000	1.0000
F81IG	40	-1414.2215	2915.4217	0.0000	1.0000
K2P	36	-1429.6958	2937.0118	0.0000	1.0000
SYM	40	-1426.2564	2939.4915	0.0000	1.0000
JC69I	36	-1435.4325	2948.4853	0.0000	1.0000
JC69G	36	-1435.5170	2948.6543	0.0000	1.0000
JC69IG	37	-1435.5167	2950.9785	0.0000	1.0000
F81	38	-1438.6197	2959.5191	0.0000	1.0000
JC69	35	-1459.9614	2995.2281	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-1377.0697	2834.1395	0.3120	0.3120
HKYG	40	-1377.3158	2834.6315	0.2440	0.5560
GTRI	44	-1373.7280	2835.4560	0.1615	0.7175
GTRG	44	-1373.8650	2835.7299	0.1409	0.8584
HKYIG	41	-1377.3155	2836.6310	0.0898	0.9482
GTRIG	45	-1373.8647	2837.7295	0.0518	1.0000
K2PI	37	-1401.8509	2877.7019	0.0000	1.0000
K2PG	37	-1402.0173	2878.0346	0.0000	1.0000
K2PIG	38	-1402.0170	2880.0341	0.0000	1.0000
SYMG	41	-1400.7354	2883.4708	0.0000	1.0000
SYMI	41	-1400.8845	2883.7690	0.0000	1.0000
GTR	43	-1399.3344	2884.6688	0.0000	1.0000
SYMIG	42	-1400.7361	2885.4723	0.0000	1.0000
HKY	39	-1404.5218	2887.0436	0.0000	1.0000
F81I	39	-1414.0456	2906.0912	0.0000	1.0000
F81G	39	-1414.2217	2906.4434	0.0000	1.0000
F81IG	40	-1414.2215	2908.4429	0.0000	1.0000
K2P	36	-1429.6958	2931.3916	0.0000	1.0000
SYM	40	-1426.2564	2932.5128	0.0000	1.0000
JC69I	36	-1435.4325	2942.8650	0.0000	1.0000
JC69G	36	-1435.5170	2943.0340	0.0000	1.0000
JC69IG	37	-1435.5167	2945.0335	0.0000	1.0000
F81	38	-1438.6197	2953.2394	0.0000	1.0000
JC69	35	-1459.9614	2989.9228	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1377.0697	3003.5943	0.5504	0.5504
HKYG	40	-1377.3158	3004.0863	0.4304	0.9808
HKYIG	41	-1377.3155	3010.3221	0.0190	0.9999
GTRI	44	-1373.7280	3021.8562	0.0001	0.9999
GTRG	44	-1373.8650	3022.1302	0.0001	1.0000
GTRIG	45	-1373.8647	3028.3661	0.0000	1.0000
K2PI	37	-1401.8509	3034.4476	0.0000	1.0000
K2PG	37	-1402.0173	3034.7803	0.0000	1.0000
K2PIG	38	-1402.0170	3041.0161	0.0000	1.0000
HKY	39	-1404.5218	3052.2620	0.0000	1.0000
SYMG	41	-1400.7354	3057.1620	0.0000	1.0000
SYMI	41	-1400.8845	3057.4601	0.0000	1.0000
SYMIG	42	-1400.7361	3063.3998	0.0000	1.0000
GTR	43	-1399.3344	3066.8327	0.0000	1.0000
F81I	39	-1414.0456	3071.3096	0.0000	1.0000
F81G	39	-1414.2217	3071.6618	0.0000	1.0000
F81IG	40	-1414.2215	3077.8977	0.0000	1.0000
K2P	36	-1429.6958	3083.9009	0.0000	1.0000
JC69I	36	-1435.4325	3095.3743	0.0000	1.0000
JC69G	36	-1435.5170	3095.5433	0.0000	1.0000
JC69IG	37	-1435.5167	3101.7792	0.0000	1.0000
SYM	40	-1426.2564	3101.9676	0.0000	1.0000
F81	38	-1438.6197	3114.2215	0.0000	1.0000
JC69	35	-1459.9614	3138.1957	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_25095.phylip = 1 - 511;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_25095.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_25095.phylip = 1 - 511;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_25095.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_25095.phylip = 1 - 511;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_25095.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

