
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:16 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_3108.phylip" (19 taxa, 557 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	-1090.6345	2267.6255	0.5594	0.5594
HKYG	40	-1091.4740	2269.3046	0.2416	0.8010
HKYIG	41	-1090.6345	2269.9564	0.1744	0.9754
GTRI	44	-1089.6341	2275.0026	0.0140	0.9894
GTRG	44	-1090.4301	2276.5946	0.0063	0.9957
GTRIG	45	-1089.6339	2277.3695	0.0043	1.0000
HKY	39	-1101.8767	2287.7882	0.0000	1.0000
GTR	43	-1100.7625	2294.9012	0.0000	1.0000
K2PI	37	-1108.4638	2296.3457	0.0000	1.0000
K2PG	37	-1108.9853	2297.3887	0.0000	1.0000
K2PIG	38	-1108.4638	2298.6496	0.0000	1.0000
F81I	39	-1107.4281	2298.8909	0.0000	1.0000
F81G	39	-1108.1289	2300.2926	0.0000	1.0000
F81IG	40	-1107.4280	2301.2125	0.0000	1.0000
SYMI	41	-1107.7916	2304.2705	0.0000	1.0000
SYMG	41	-1108.2154	2305.1181	0.0000	1.0000
SYMIG	42	-1107.7916	2306.6104	0.0000	1.0000
K2P	36	-1118.6954	2314.5140	0.0000	1.0000
F81	38	-1118.1810	2318.0841	0.0000	1.0000
SYM	40	-1117.6878	2321.7322	0.0000	1.0000
JC69I	36	-1123.7245	2324.5720	0.0000	1.0000
JC69G	36	-1124.2922	2325.7074	0.0000	1.0000
JC69IG	37	-1123.7250	2326.8681	0.0000	1.0000
JC69	35	-1134.0537	2342.9442	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-1090.6345	2261.2689	0.5290	0.5290
HKYG	40	-1091.4740	2262.9480	0.2285	0.7575
HKYIG	41	-1090.6345	2263.2690	0.1946	0.9521
GTRI	44	-1089.6341	2267.2682	0.0263	0.9784
GTRG	44	-1090.4301	2268.8602	0.0119	0.9903
GTRIG	45	-1089.6339	2269.2678	0.0097	1.0000
HKY	39	-1101.8767	2281.7534	0.0000	1.0000
GTR	43	-1100.7625	2287.5249	0.0000	1.0000
K2PI	37	-1108.4638	2290.9275	0.0000	1.0000
K2PG	37	-1108.9853	2291.9706	0.0000	1.0000
F81I	39	-1107.4281	2292.8561	0.0000	1.0000
K2PIG	38	-1108.4638	2292.9276	0.0000	1.0000
F81G	39	-1108.1289	2294.2578	0.0000	1.0000
F81IG	40	-1107.4280	2294.8559	0.0000	1.0000
SYMI	41	-1107.7916	2297.5831	0.0000	1.0000
SYMG	41	-1108.2154	2298.4308	0.0000	1.0000
SYMIG	42	-1107.7916	2299.5832	0.0000	1.0000
K2P	36	-1118.6954	2309.3909	0.0000	1.0000
F81	38	-1118.1810	2312.3621	0.0000	1.0000
SYM	40	-1117.6878	2315.3756	0.0000	1.0000
JC69I	36	-1123.7245	2319.4490	0.0000	1.0000
JC69G	36	-1124.2922	2320.5843	0.0000	1.0000
JC69IG	37	-1123.7250	2321.4500	0.0000	1.0000
JC69	35	-1134.0537	2338.1073	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1090.6345	2434.1715	0.6780	0.6780
HKYG	40	-1091.4740	2435.8506	0.2928	0.9708
HKYIG	41	-1090.6345	2440.4942	0.0287	0.9995
HKY	39	-1101.8767	2450.3334	0.0002	0.9997
K2PI	37	-1108.4638	2450.8625	0.0002	0.9999
K2PG	37	-1108.9853	2451.9055	0.0001	1.0000
K2PIG	38	-1108.4638	2457.1851	0.0000	1.0000
GTRI	44	-1089.6341	2457.4611	0.0000	1.0000
GTRG	44	-1090.4301	2459.0531	0.0000	1.0000
F81I	39	-1107.4281	2461.4362	0.0000	1.0000
F81G	39	-1108.1289	2462.8378	0.0000	1.0000
GTRIG	45	-1089.6339	2463.7832	0.0000	1.0000
K2P	36	-1118.6954	2465.0032	0.0000	1.0000
F81IG	40	-1107.4280	2467.7585	0.0000	1.0000
GTR	43	-1100.7625	2473.3952	0.0000	1.0000
SYMI	41	-1107.7916	2474.8083	0.0000	1.0000
JC69I	36	-1123.7245	2475.0613	0.0000	1.0000
SYMG	41	-1108.2154	2475.6559	0.0000	1.0000
JC69G	36	-1124.2922	2476.1967	0.0000	1.0000
F81	38	-1118.1810	2476.6196	0.0000	1.0000
SYMIG	42	-1107.7916	2481.1309	0.0000	1.0000
JC69IG	37	-1123.7250	2481.3849	0.0000	1.0000
SYM	40	-1117.6878	2488.2782	0.0000	1.0000
JC69	35	-1134.0537	2489.3971	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/chr11_3108.phylip = 1 - 557;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3108.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/chr11_3108.phylip = 1 - 557;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3108.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/chr11_3108.phylip = 1 - 557;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3108.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

