
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:48 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/chr7_1360.phylip" (19 taxa, 415 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: SYMG
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
SYMG	41	-1395.3004	2881.8340	0.2550	0.2550
GTRIG	45	-1390.3600	2881.9394	0.2419	0.4969
GTRG	44	-1391.8747	2882.4521	0.1872	0.6841
SYMI	41	-1395.9271	2883.0875	0.1363	0.8204
GTRI	44	-1392.4677	2883.6380	0.1035	0.9239
SYMIG	42	-1395.2905	2884.2906	0.0747	0.9985
HKYG	40	-1402.4542	2893.6785	0.0007	0.9992
K2PG	37	-1406.9470	2895.3529	0.0003	0.9995
HKYIG	41	-1402.4523	2896.1377	0.0002	0.9997
HKYI	40	-1404.1525	2897.0750	0.0001	0.9998
K2PIG	38	-1406.9489	2897.7807	0.0001	0.9999
K2PI	37	-1408.4052	2898.2694	0.0001	1.0000
SYM	40	-1409.2450	2907.2602	0.0000	1.0000
GTR	43	-1405.9048	2908.0090	0.0000	1.0000
HKY	39	-1417.5297	2921.3794	0.0000	1.0000
K2P	36	-1421.9545	2922.9567	0.0000	1.0000
F81G	39	-1428.6271	2943.5742	0.0000	1.0000
F81I	39	-1429.7130	2945.7460	0.0000	1.0000
F81IG	40	-1428.6301	2946.0303	0.0000	1.0000
JC69G	36	-1433.7646	2946.5767	0.0000	1.0000
JC69I	36	-1434.7329	2948.5134	0.0000	1.0000
JC69IG	37	-1433.7673	2948.9934	0.0000	1.0000
F81	38	-1442.5288	2968.9405	0.0000	1.0000
JC69	35	-1447.3614	2971.3719	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1390.3600	2870.7199	0.3740	0.3740
GTRG	44	-1391.8747	2871.7494	0.2235	0.5975
SYMG	41	-1395.3004	2872.6007	0.1460	0.7436
GTRI	44	-1392.4677	2872.9353	0.1235	0.8671
SYMI	41	-1395.9271	2873.8543	0.0780	0.9451
SYMIG	42	-1395.2905	2874.5809	0.0543	0.9994
HKYG	40	-1402.4542	2884.9085	0.0003	0.9997
HKYIG	41	-1402.4523	2886.9045	0.0001	0.9998
K2PG	37	-1406.9470	2887.8940	0.0001	0.9999
HKYI	40	-1404.1525	2888.3050	0.0001	1.0000
K2PIG	38	-1406.9489	2889.8978	0.0000	1.0000
K2PI	37	-1408.4052	2890.8105	0.0000	1.0000
GTR	43	-1405.9048	2897.8096	0.0000	1.0000
SYM	40	-1409.2450	2898.4901	0.0000	1.0000
HKY	39	-1417.5297	2913.0594	0.0000	1.0000
K2P	36	-1421.9545	2915.9091	0.0000	1.0000
F81G	39	-1428.6271	2935.2542	0.0000	1.0000
F81IG	40	-1428.6301	2937.2602	0.0000	1.0000
F81I	39	-1429.7130	2937.4260	0.0000	1.0000
JC69G	36	-1433.7646	2939.5291	0.0000	1.0000
JC69I	36	-1434.7329	2941.4658	0.0000	1.0000
JC69IG	37	-1433.7673	2941.5345	0.0000	1.0000
F81	38	-1442.5288	2961.0575	0.0000	1.0000
JC69	35	-1447.3614	2964.7229	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1406.9470	3036.9403	0.4255	0.4255
SYMG	41	-1395.3004	3037.7601	0.2824	0.7079
SYMI	41	-1395.9271	3039.0137	0.1509	0.8588
K2PI	37	-1408.4052	3039.8568	0.0990	0.9578
K2PIG	38	-1406.9489	3042.9723	0.0208	0.9786
SYMIG	42	-1395.2905	3043.7686	0.0140	0.9926
HKYG	40	-1402.4542	3046.0396	0.0045	0.9971
GTRG	44	-1391.8747	3048.9937	0.0010	0.9982
HKYI	40	-1404.1525	3049.4361	0.0008	0.9990
GTRI	44	-1392.4677	3050.1796	0.0006	0.9995
GTRIG	45	-1390.3600	3051.9925	0.0002	0.9998
HKYIG	41	-1402.4523	3052.0639	0.0002	1.0000
SYM	40	-1409.2450	3059.6212	0.0000	1.0000
K2P	36	-1421.9545	3060.9271	0.0000	1.0000
HKY	39	-1417.5297	3070.1622	0.0000	1.0000
GTR	43	-1405.9048	3071.0255	0.0000	1.0000
JC69G	36	-1433.7646	3084.5471	0.0000	1.0000
JC69I	36	-1434.7329	3086.4838	0.0000	1.0000
JC69IG	37	-1433.7673	3090.5808	0.0000	1.0000
F81G	39	-1428.6271	3092.3571	0.0000	1.0000
F81I	39	-1429.7130	3094.5289	0.0000	1.0000
F81IG	40	-1428.6301	3098.3914	0.0000	1.0000
JC69	35	-1447.3614	3105.7126	0.0000	1.0000
F81	38	-1442.5288	3114.1321	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/chr7_1360.phylip = 1 - 415;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1360.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 (SYMG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1360.phylip = 1 - 415;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1360.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=Fixed(Equal);
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/chr7_1360.phylip = 1 - 415;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1360.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;


-------------------------------------------------------------
End of Output

