
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:44 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/chr5_14870.phylip" (19 taxa, 417 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	-1280.9483	2650.6199	0.3853	0.3853
HKYIG	41	-1280.7405	2652.6649	0.1386	0.5239
K2PG	37	-1285.6502	2652.7199	0.1348	0.6588
GTRG	44	-1277.0985	2652.8421	0.1269	0.7856
HKYI	40	-1282.5432	2653.8099	0.0782	0.8638
GTRIG	45	-1276.8078	2654.7747	0.0483	0.9121
K2PIG	38	-1285.8862	2655.6137	0.0317	0.9438
GTRI	44	-1278.8073	2656.2598	0.0230	0.9668
K2PI	37	-1287.6502	2656.7199	0.0182	0.9851
SYMG	41	-1283.3212	2657.8264	0.0105	0.9955
SYMIG	42	-1283.3753	2660.4083	0.0029	0.9984
SYMI	41	-1285.2255	2661.6350	0.0016	1.0000
HKY	39	-1294.8659	2676.0076	0.0000	1.0000
F81G	39	-1295.0689	2676.4136	0.0000	1.0000
JC69G	36	-1299.3513	2677.7132	0.0000	1.0000
GTR	43	-1291.2284	2678.6016	0.0000	1.0000
K2P	36	-1299.7964	2678.6033	0.0000	1.0000
F81IG	40	-1295.0325	2678.7884	0.0000	1.0000
F81I	39	-1296.6332	2679.5422	0.0000	1.0000
JC69IG	37	-1299.7072	2680.8340	0.0000	1.0000
JC69I	36	-1301.3581	2681.7267	0.0000	1.0000
SYM	40	-1297.6487	2684.0208	0.0000	1.0000
F81	38	-1308.6127	2701.0667	0.0000	1.0000
JC69	35	-1313.1004	2702.8150	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1280.9483	2641.8965	0.2935	0.2935
GTRG	44	-1277.0985	2642.1969	0.2526	0.5461
HKYIG	41	-1280.7405	2643.4809	0.1329	0.6790
GTRIG	45	-1276.8078	2643.6157	0.1243	0.8033
HKYI	40	-1282.5432	2645.0865	0.0596	0.8629
K2PG	37	-1285.6502	2645.3004	0.0535	0.9164
GTRI	44	-1278.8073	2645.6147	0.0457	0.9621
K2PIG	38	-1285.8862	2647.7724	0.0155	0.9777
SYMG	41	-1283.3212	2648.6424	0.0101	0.9877
K2PI	37	-1287.6502	2649.3003	0.0072	0.9950
SYMIG	42	-1283.3753	2650.7505	0.0035	0.9985
SYMI	41	-1285.2255	2652.4510	0.0015	1.0000
HKY	39	-1294.8659	2667.7317	0.0000	1.0000
F81G	39	-1295.0689	2668.1377	0.0000	1.0000
GTR	43	-1291.2284	2668.4568	0.0000	1.0000
F81IG	40	-1295.0325	2670.0650	0.0000	1.0000
JC69G	36	-1299.3513	2670.7027	0.0000	1.0000
F81I	39	-1296.6332	2671.2663	0.0000	1.0000
K2P	36	-1299.7964	2671.5928	0.0000	1.0000
JC69IG	37	-1299.7072	2673.4145	0.0000	1.0000
JC69I	36	-1301.3581	2674.7162	0.0000	1.0000
SYM	40	-1297.6487	2675.2974	0.0000	1.0000
F81	38	-1308.6127	2693.2255	0.0000	1.0000
JC69	35	-1313.1004	2696.2008	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1285.6502	2794.5246	0.8400	0.8400
K2PI	37	-1287.6502	2798.5245	0.1137	0.9537
K2PIG	38	-1285.8862	2801.0297	0.0325	0.9862
HKYG	40	-1280.9483	2803.2200	0.0109	0.9970
HKYI	40	-1282.5432	2806.4099	0.0022	0.9992
HKYIG	41	-1280.7405	2808.8375	0.0007	0.9999
SYMG	41	-1283.3212	2813.9989	0.0000	1.0000
JC69G	36	-1299.3513	2815.8938	0.0000	1.0000
K2P	36	-1299.7964	2816.7839	0.0000	1.0000
SYMI	41	-1285.2255	2817.8076	0.0000	1.0000
GTRG	44	-1277.0985	2819.6527	0.0000	1.0000
JC69I	36	-1301.3581	2819.9073	0.0000	1.0000
SYMIG	42	-1283.3753	2820.1401	0.0000	1.0000
JC69IG	37	-1299.7072	2822.6387	0.0000	1.0000
GTRI	44	-1278.8073	2823.0705	0.0000	1.0000
HKY	39	-1294.8659	2825.0221	0.0000	1.0000
GTRIG	45	-1276.8078	2825.1045	0.0000	1.0000
F81G	39	-1295.0689	2825.4281	0.0000	1.0000
F81I	39	-1296.6332	2828.5567	0.0000	1.0000
F81IG	40	-1295.0325	2831.3884	0.0000	1.0000
SYM	40	-1297.6487	2836.6208	0.0000	1.0000
JC69	35	-1313.1004	2837.3589	0.0000	1.0000
GTR	43	-1291.2284	2841.8795	0.0000	1.0000
F81	38	-1308.6127	2846.4827	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/chr5_14870.phylip = 1 - 417;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_14870.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/chr5_14870.phylip = 1 - 417;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_14870.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/chr5_14870.phylip = 1 - 417;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_14870.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

