
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:07 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/chr19_329.phylip" (19 taxa, 439 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRG
Minimum BIC  model: HKYG


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	-1272.6140	2643.2787	0.3109	0.3109
GTRIG	45	-1271.3884	2643.3111	0.3059	0.6168
HKYG	40	-1277.8792	2643.9997	0.2168	0.8337
HKYIG	41	-1276.9801	2644.6352	0.1578	0.9914
HKYI	40	-1281.2990	2650.8391	0.0071	0.9985
GTRI	44	-1277.9788	2654.0084	0.0015	1.0000
K2PG	37	-1293.4500	2667.9125	0.0000	1.0000
K2PIG	38	-1292.5318	2668.4736	0.0000	1.0000
SYMG	41	-1290.3209	2671.3169	0.0000	1.0000
SYMIG	42	-1289.1923	2671.5059	0.0000	1.0000
K2PI	37	-1296.8918	2674.7960	0.0000	1.0000
SYMI	41	-1294.0653	2678.8057	0.0000	1.0000
HKY	39	-1307.0645	2699.9485	0.0000	1.0000
GTR	43	-1303.3749	2702.3295	0.0000	1.0000
F81G	39	-1313.6285	2713.0766	0.0000	1.0000
F81IG	40	-1312.7840	2713.8091	0.0000	1.0000
F81I	39	-1317.0488	2719.9172	0.0000	1.0000
K2P	36	-1322.3797	2723.3862	0.0000	1.0000
SYM	40	-1320.4163	2729.0738	0.0000	1.0000
JC69G	36	-1330.0214	2738.6697	0.0000	1.0000
JC69IG	37	-1329.1345	2739.2815	0.0000	1.0000
JC69I	36	-1333.3828	2745.3924	0.0000	1.0000
F81	38	-1341.2022	2765.8144	0.0000	1.0000
JC69	35	-1358.0602	2792.3735	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1271.3884	2632.7768	0.4468	0.4468
GTRG	44	-1272.6140	2633.2279	0.3566	0.8034
HKYG	40	-1277.8792	2635.7585	0.1006	0.9041
HKYIG	41	-1276.9801	2635.9601	0.0910	0.9950
HKYI	40	-1281.2990	2642.5979	0.0033	0.9983
GTRI	44	-1277.9788	2643.9576	0.0017	1.0000
K2PG	37	-1293.4500	2660.9001	0.0000	1.0000
K2PIG	38	-1292.5318	2661.0636	0.0000	1.0000
SYMIG	42	-1289.1923	2662.3846	0.0000	1.0000
SYMG	41	-1290.3209	2662.6418	0.0000	1.0000
K2PI	37	-1296.8918	2667.7835	0.0000	1.0000
SYMI	41	-1294.0653	2670.1307	0.0000	1.0000
HKY	39	-1307.0645	2692.1289	0.0000	1.0000
GTR	43	-1303.3749	2692.7498	0.0000	1.0000
F81G	39	-1313.6285	2705.2570	0.0000	1.0000
F81IG	40	-1312.7840	2705.5679	0.0000	1.0000
F81I	39	-1317.0488	2712.0977	0.0000	1.0000
K2P	36	-1322.3797	2716.7593	0.0000	1.0000
SYM	40	-1320.4163	2720.8326	0.0000	1.0000
JC69G	36	-1330.0214	2732.0428	0.0000	1.0000
JC69IG	37	-1329.1345	2732.2690	0.0000	1.0000
JC69I	36	-1333.3828	2738.7656	0.0000	1.0000
F81	38	-1341.2022	2758.4044	0.0000	1.0000
JC69	35	-1358.0602	2786.1204	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1277.8792	2799.1385	0.8673	0.8673
HKYIG	41	-1276.9801	2803.4246	0.1017	0.9690
HKYI	40	-1281.2990	2805.9779	0.0284	0.9974
K2PG	37	-1293.4500	2812.0266	0.0014	0.9988
GTRG	44	-1272.6140	2812.9459	0.0009	0.9996
K2PIG	38	-1292.5318	2816.2746	0.0002	0.9998
GTRIG	45	-1271.3884	2816.5793	0.0001	1.0000
K2PI	37	-1296.8918	2818.9100	0.0000	1.0000
GTRI	44	-1277.9788	2823.6756	0.0000	1.0000
SYMG	41	-1290.3209	2830.1063	0.0000	1.0000
SYMIG	42	-1289.1923	2833.9336	0.0000	1.0000
SYMI	41	-1294.0653	2837.5952	0.0000	1.0000
HKY	39	-1307.0645	2851.4244	0.0000	1.0000
K2P	36	-1322.3797	2863.8013	0.0000	1.0000
F81G	39	-1313.6285	2864.5525	0.0000	1.0000
GTR	43	-1303.3749	2868.3832	0.0000	1.0000
F81IG	40	-1312.7840	2868.9479	0.0000	1.0000
F81I	39	-1317.0488	2871.3931	0.0000	1.0000
JC69G	36	-1330.0214	2879.0848	0.0000	1.0000
JC69IG	37	-1329.1345	2883.3955	0.0000	1.0000
SYM	40	-1320.4163	2884.2126	0.0000	1.0000
JC69I	36	-1333.3828	2885.8075	0.0000	1.0000
F81	38	-1341.2022	2913.6154	0.0000	1.0000
JC69	35	-1358.0602	2929.0779	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_329.phylip = 1 - 439;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_329.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr19_329.phylip = 1 - 439;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_329.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_329.phylip = 1 - 439;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_329.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;


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End of Output

