
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:37 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/chr1_19885.phylip" (19 taxa, 387 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-1286.8213	2663.1224	0.4890	0.4890
HKYI	40	-1287.2541	2663.9880	0.3172	0.8063
HKYIG	41	-1286.8257	2665.6340	0.1393	0.9456
GTRG	44	-1285.3307	2670.2403	0.0139	0.9595
K2PG	37	-1294.4107	2670.8788	0.0101	0.9696
GTRI	44	-1285.7374	2671.0536	0.0093	0.9789
K2PI	37	-1294.6327	2671.3227	0.0081	0.9870
GTRIG	45	-1285.3399	2672.8205	0.0038	0.9908
SYMG	41	-1290.6300	2673.2426	0.0031	0.9939
K2PIG	38	-1294.4261	2673.3694	0.0029	0.9968
SYMI	41	-1290.9313	2673.8452	0.0023	0.9991
SYMIG	42	-1290.6365	2675.7730	0.0009	1.0000
HKY	39	-1301.4858	2689.9630	0.0000	1.0000
F81G	39	-1303.4527	2693.8967	0.0000	1.0000
F81I	39	-1303.7393	2694.4700	0.0000	1.0000
GTR	43	-1299.6530	2696.3382	0.0000	1.0000
F81IG	40	-1303.4617	2696.4031	0.0000	1.0000
K2P	36	-1308.8793	2697.3701	0.0000	1.0000
SYM	40	-1304.8378	2699.1554	0.0000	1.0000
JC69G	36	-1311.9669	2703.5452	0.0000	1.0000
JC69I	36	-1312.1694	2703.9501	0.0000	1.0000
JC69IG	37	-1311.9816	2706.0205	0.0000	1.0000
F81	38	-1317.8070	2720.1313	0.0000	1.0000
JC69	35	-1325.5378	2728.2551	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1286.8213	2653.6426	0.4506	0.4506
HKYI	40	-1287.2541	2654.5082	0.2923	0.7429
HKYIG	41	-1286.8257	2655.6514	0.1650	0.9080
GTRG	44	-1285.3307	2658.6613	0.0366	0.9446
GTRI	44	-1285.7374	2659.4747	0.0244	0.9690
GTRIG	45	-1285.3399	2660.6797	0.0134	0.9824
K2PG	37	-1294.4107	2662.8215	0.0046	0.9869
SYMG	41	-1290.6300	2663.2600	0.0037	0.9906
K2PI	37	-1294.6327	2663.2654	0.0037	0.9943
SYMI	41	-1290.9313	2663.8626	0.0027	0.9970
K2PIG	38	-1294.4261	2664.8522	0.0017	0.9987
SYMIG	42	-1290.6365	2665.2730	0.0013	1.0000
HKY	39	-1301.4858	2680.9716	0.0000	1.0000
F81G	39	-1303.4527	2684.9053	0.0000	1.0000
GTR	43	-1299.6530	2685.3061	0.0000	1.0000
F81I	39	-1303.7393	2685.4787	0.0000	1.0000
F81IG	40	-1303.4617	2686.9233	0.0000	1.0000
SYM	40	-1304.8378	2689.6756	0.0000	1.0000
K2P	36	-1308.8793	2689.7586	0.0000	1.0000
JC69G	36	-1311.9669	2695.9338	0.0000	1.0000
JC69I	36	-1312.1694	2696.3387	0.0000	1.0000
JC69IG	37	-1311.9816	2697.9632	0.0000	1.0000
F81	38	-1317.8070	2711.6140	0.0000	1.0000
JC69	35	-1325.5378	2721.0756	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1294.4107	2809.2832	0.4361	0.4361
K2PI	37	-1294.6327	2809.7272	0.3493	0.7855
HKYG	40	-1286.8213	2811.9796	0.1133	0.8987
HKYI	40	-1287.2541	2812.8452	0.0735	0.9722
K2PIG	38	-1294.4261	2815.2723	0.0218	0.9940
HKYIG	41	-1286.8257	2817.9469	0.0057	0.9998
SYMG	41	-1290.6300	2825.5554	0.0001	0.9999
SYMI	41	-1290.9313	2826.1580	0.0001	1.0000
SYMIG	42	-1290.6365	2831.5268	0.0000	1.0000
K2P	36	-1308.8793	2832.2619	0.0000	1.0000
GTRG	44	-1285.3307	2832.8320	0.0000	1.0000
GTRI	44	-1285.7374	2833.6454	0.0000	1.0000
HKY	39	-1301.4858	2835.3502	0.0000	1.0000
JC69G	36	-1311.9669	2838.4371	0.0000	1.0000
GTRIG	45	-1285.3399	2838.8089	0.0000	1.0000
JC69I	36	-1312.1694	2838.8420	0.0000	1.0000
F81G	39	-1303.4527	2839.2839	0.0000	1.0000
F81I	39	-1303.7393	2839.8572	0.0000	1.0000
JC69IG	37	-1311.9816	2844.4250	0.0000	1.0000
F81IG	40	-1303.4617	2845.2603	0.0000	1.0000
SYM	40	-1304.8378	2848.0126	0.0000	1.0000
GTR	43	-1299.6530	2855.5184	0.0000	1.0000
JC69	35	-1325.5378	2859.6204	0.0000	1.0000
F81	38	-1317.8070	2862.0342	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_19885.phylip = 1 - 387;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_19885.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_19885.phylip = 1 - 387;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_19885.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;


[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/chr1_19885.phylip = 1 - 387;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_19885.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

