
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:09 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/chr3_18950.phylip" (19 taxa, 266 characters)

Minimum AIC  model: GTRG
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	-1227.6825	2561.2837	0.4600	0.4600
HKYG	40	-1234.0387	2562.6552	0.2317	0.6917
GTRIG	45	-1227.3967	2563.6116	0.1436	0.8353
HKYIG	41	-1233.8459	2565.0668	0.0694	0.9047
GTRI	44	-1229.9033	2565.7251	0.0499	0.9546
HKYI	40	-1235.7210	2566.0197	0.0431	0.9977
K2PG	37	-1242.9689	2572.2711	0.0019	0.9996
SYMG	41	-1240.1031	2577.5812	0.0001	0.9998
K2PIG	38	-1244.3710	2577.7993	0.0001	0.9999
K2PI	37	-1246.2804	2578.8941	0.0001	0.9999
SYMIG	42	-1239.9820	2580.1613	0.0000	1.0000
SYMI	41	-1242.0744	2581.5239	0.0000	1.0000
GTR	43	-1258.4981	2620.0413	0.0000	1.0000
HKY	39	-1264.4432	2620.6916	0.0000	1.0000
K2P	36	-1274.3857	2632.4045	0.0000	1.0000
SYM	40	-1270.6796	2635.9370	0.0000	1.0000
F81G	39	-1274.3276	2640.4605	0.0000	1.0000
F81IG	40	-1273.9208	2642.4195	0.0000	1.0000
F81I	39	-1275.8646	2643.5345	0.0000	1.0000
JC69G	36	-1285.0711	2653.7753	0.0000	1.0000
JC69IG	37	-1284.7117	2655.7567	0.0000	1.0000
JC69I	36	-1286.5856	2656.8044	0.0000	1.0000
F81	38	-1302.3055	2693.6682	0.0000	1.0000
JC69	35	-1313.1525	2707.2615	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1227.6825	2543.3651	0.5704	0.5704
GTRIG	45	-1227.3967	2544.7934	0.2793	0.8496
GTRI	44	-1229.9033	2547.8066	0.0619	0.9115
HKYG	40	-1234.0387	2548.0774	0.0541	0.9656
HKYIG	41	-1233.8459	2549.6918	0.0241	0.9897
HKYI	40	-1235.7210	2551.4419	0.0101	0.9998
K2PG	37	-1242.9689	2559.9378	0.0001	0.9999
SYMG	41	-1240.1031	2562.2062	0.0000	1.0000
SYMIG	42	-1239.9820	2563.9640	0.0000	1.0000
K2PIG	38	-1244.3710	2564.7421	0.0000	1.0000
SYMI	41	-1242.0744	2566.1489	0.0000	1.0000
K2PI	37	-1246.2804	2566.5608	0.0000	1.0000
GTR	43	-1258.4981	2602.9963	0.0000	1.0000
HKY	39	-1264.4432	2606.8863	0.0000	1.0000
K2P	36	-1274.3857	2620.7713	0.0000	1.0000
SYM	40	-1270.6796	2621.3592	0.0000	1.0000
F81G	39	-1274.3276	2626.6552	0.0000	1.0000
F81IG	40	-1273.9208	2627.8417	0.0000	1.0000
F81I	39	-1275.8646	2629.7292	0.0000	1.0000
JC69G	36	-1285.0711	2642.1421	0.0000	1.0000
JC69IG	37	-1284.7117	2643.4234	0.0000	1.0000
JC69I	36	-1286.5856	2645.1712	0.0000	1.0000
F81	38	-1302.3055	2680.6110	0.0000	1.0000
JC69	35	-1313.1525	2696.3050	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1234.0387	2691.4173	0.5337	0.5337
K2PG	37	-1242.9689	2692.5271	0.3064	0.8400
HKYI	40	-1235.7210	2694.7818	0.0992	0.9393
HKYIG	41	-1233.8459	2696.6152	0.0397	0.9789
K2PI	37	-1246.2804	2699.1501	0.0112	0.9901
K2PIG	38	-1244.3710	2700.9149	0.0046	0.9947
GTRG	44	-1227.6825	2701.0389	0.0043	0.9991
GTRI	44	-1229.9033	2705.4804	0.0005	0.9996
GTRIG	45	-1227.3967	2706.0508	0.0004	0.9999
SYMG	41	-1240.1031	2709.1295	0.0001	1.0000
SYMI	41	-1242.0744	2713.0722	0.0000	1.0000
SYMIG	42	-1239.9820	2714.4709	0.0000	1.0000
HKY	39	-1264.4432	2746.6427	0.0000	1.0000
K2P	36	-1274.3857	2749.7772	0.0000	1.0000
GTR	43	-1258.4981	2757.0866	0.0000	1.0000
SYM	40	-1270.6796	2764.6991	0.0000	1.0000
F81G	39	-1274.3276	2766.4116	0.0000	1.0000
F81I	39	-1275.8646	2769.4856	0.0000	1.0000
JC69G	36	-1285.0711	2771.1480	0.0000	1.0000
F81IG	40	-1273.9208	2771.1815	0.0000	1.0000
JC69I	36	-1286.5856	2774.1770	0.0000	1.0000
JC69IG	37	-1284.7117	2776.0127	0.0000	1.0000
F81	38	-1302.3055	2816.7838	0.0000	1.0000
JC69	35	-1313.1525	2821.7274	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/chr3_18950.phylip = 1 - 266;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_18950.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/chr3_18950.phylip = 1 - 266;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_18950.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/chr3_18950.phylip = 1 - 266;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_18950.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

