
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:06 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/chr10_4885.phylip" (19 taxa, 375 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1278.3370	2656.6740	0.6511	0.6511
GTRIG	45	-1277.9676	2658.5189	0.2588	0.9099
GTRI	44	-1280.9892	2661.9784	0.0459	0.9558
HKYG	40	-1286.8975	2663.6154	0.0202	0.9760
HKYIG	41	-1286.5256	2665.3936	0.0083	0.9844
HKYI	40	-1288.3912	2666.6028	0.0045	0.9889
SYMG	41	-1287.2249	2666.7921	0.0041	0.9930
K2PG	37	-1292.6484	2667.6410	0.0027	0.9957
SYMIG	42	-1286.7629	2668.4053	0.0018	0.9976
K2PIG	38	-1292.2241	2669.2697	0.0012	0.9988
K2PI	37	-1294.0000	2670.3443	0.0007	0.9995
SYMI	41	-1289.3031	2670.9486	0.0005	1.0000
GTR	43	-1299.0748	2695.5816	0.0000	1.0000
HKY	39	-1309.7694	2706.8522	0.0000	1.0000
SYM	40	-1310.4361	2710.6925	0.0000	1.0000
K2P	36	-1318.0551	2715.9918	0.0000	1.0000
F81G	39	-1322.4696	2732.2526	0.0000	1.0000
JC69G	36	-1327.8360	2735.5536	0.0000	1.0000
F81IG	40	-1324.0239	2737.8681	0.0000	1.0000
JC69IG	37	-1329.5084	2741.3611	0.0000	1.0000
JC69I	36	-1331.0215	2741.9246	0.0000	1.0000
F81I	39	-1328.0768	2743.4671	0.0000	1.0000
F81	38	-1347.5529	2779.9272	0.0000	1.0000
JC69	35	-1354.0252	2785.4840	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1278.3370	2644.6740	0.6146	0.6146
GTRIG	45	-1277.9676	2645.9353	0.3271	0.9417
GTRI	44	-1280.9892	2649.9784	0.0433	0.9850
HKYG	40	-1286.8975	2653.7950	0.0064	0.9915
HKYIG	41	-1286.5256	2655.0512	0.0034	0.9949
SYMG	41	-1287.2249	2656.4498	0.0017	0.9966
HKYI	40	-1288.3912	2656.7825	0.0014	0.9980
SYMIG	42	-1286.7629	2657.5258	0.0010	0.9990
K2PG	37	-1292.6484	2659.2967	0.0004	0.9994
K2PIG	38	-1292.2241	2660.4483	0.0002	0.9997
SYMI	41	-1289.3031	2660.6062	0.0002	0.9999
K2PI	37	-1294.0000	2662.0001	0.0001	1.0000
GTR	43	-1299.0748	2684.1496	0.0000	1.0000
HKY	39	-1309.7694	2697.5388	0.0000	1.0000
SYM	40	-1310.4361	2700.8722	0.0000	1.0000
K2P	36	-1318.0551	2708.1102	0.0000	1.0000
F81G	39	-1322.4696	2722.9392	0.0000	1.0000
JC69G	36	-1327.8360	2727.6719	0.0000	1.0000
F81IG	40	-1324.0239	2728.0477	0.0000	1.0000
JC69IG	37	-1329.5084	2733.0168	0.0000	1.0000
JC69I	36	-1331.0215	2734.0430	0.0000	1.0000
F81I	39	-1328.0768	2734.1536	0.0000	1.0000
F81	38	-1347.5529	2771.1058	0.0000	1.0000
JC69	35	-1354.0252	2778.0504	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1292.6484	2804.5930	0.7154	0.7154
K2PI	37	-1294.0000	2807.2963	0.1852	0.9006
K2PIG	38	-1292.2241	2809.6714	0.0565	0.9570
HKYG	40	-1286.8975	2810.8720	0.0310	0.9880
HKYI	40	-1288.3912	2813.8595	0.0070	0.9950
HKYIG	41	-1286.5256	2816.0552	0.0023	0.9973
SYMG	41	-1287.2249	2817.4538	0.0012	0.9984
GTRG	44	-1278.3370	2817.4588	0.0012	0.9996
SYMI	41	-1289.3031	2821.6102	0.0001	0.9997
SYMIG	42	-1286.7629	2822.4567	0.0001	0.9998
GTRIG	45	-1277.9676	2822.6470	0.0001	0.9999
GTRI	44	-1280.9892	2822.7631	0.0001	1.0000
K2P	36	-1318.0551	2849.4795	0.0000	1.0000
HKY	39	-1309.7694	2850.6889	0.0000	1.0000
GTR	43	-1299.0748	2853.0074	0.0000	1.0000
SYM	40	-1310.4361	2857.9492	0.0000	1.0000
JC69G	36	-1327.8360	2869.0413	0.0000	1.0000
JC69I	36	-1331.0215	2875.4123	0.0000	1.0000
F81G	39	-1322.4696	2876.0893	0.0000	1.0000
JC69IG	37	-1329.5084	2878.3131	0.0000	1.0000
F81IG	40	-1324.0239	2885.1248	0.0000	1.0000
F81I	39	-1328.0768	2887.3038	0.0000	1.0000
JC69	35	-1354.0252	2915.4928	0.0000	1.0000
F81	38	-1347.5529	2920.3290	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/chr10_4885.phylip = 1 - 375;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4885.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/chr10_4885.phylip = 1 - 375;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4885.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4885.phylip = 1 - 375;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4885.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;


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End of Output

