
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:49 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_6276.phylip" (19 taxa, 680 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	-1376.5639	2847.3640	0.5696	0.5696
GTRI	44	-1377.1310	2848.4981	0.3231	0.8926
GTRIG	45	-1377.1310	2850.7919	0.1026	0.9952
HKYG	40	-1386.6304	2858.3939	0.0023	0.9975
HKYI	40	-1386.8555	2858.8440	0.0018	0.9994
HKYIG	41	-1386.8559	2861.1099	0.0006	1.0000
SYMI	41	-1389.9696	2867.3373	0.0000	1.0000
SYMIG	42	-1389.9696	2869.6095	0.0000	1.0000
SYMG	41	-1391.2416	2869.8813	0.0000	1.0000
K2PI	37	-1398.7101	2875.8003	0.0000	1.0000
K2PIG	38	-1398.7101	2878.0441	0.0000	1.0000
K2PG	37	-1400.4437	2879.2675	0.0000	1.0000
GTR	43	-1395.0521	2882.0540	0.0000	1.0000
HKY	39	-1404.7277	2892.3304	0.0000	1.0000
SYM	40	-1409.7285	2904.5900	0.0000	1.0000
K2P	36	-1418.4971	2913.1374	0.0000	1.0000
F81G	39	-1433.8401	2950.5553	0.0000	1.0000
F81I	39	-1434.6044	2952.0838	0.0000	1.0000
F81IG	40	-1434.6046	2954.3421	0.0000	1.0000
JC69I	36	-1445.3807	2966.9044	0.0000	1.0000
JC69G	36	-1445.8994	2967.9419	0.0000	1.0000
JC69IG	37	-1445.3765	2969.1331	0.0000	1.0000
F81	38	-1449.6927	2980.0094	0.0000	1.0000
JC69	35	-1461.8066	2997.5263	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1376.5639	2841.1278	0.5616	0.5616
GTRI	44	-1377.1310	2842.2619	0.3185	0.8801
GTRIG	45	-1377.1310	2844.2620	0.1172	0.9972
HKYG	40	-1386.6304	2853.2608	0.0013	0.9985
HKYI	40	-1386.8555	2853.7110	0.0010	0.9996
HKYIG	41	-1386.8559	2855.7117	0.0004	1.0000
SYMI	41	-1389.9696	2861.9391	0.0000	1.0000
SYMIG	42	-1389.9696	2863.9391	0.0000	1.0000
SYMG	41	-1391.2416	2864.4832	0.0000	1.0000
K2PI	37	-1398.7101	2871.4202	0.0000	1.0000
K2PIG	38	-1398.7101	2873.4201	0.0000	1.0000
K2PG	37	-1400.4437	2874.8874	0.0000	1.0000
GTR	43	-1395.0521	2876.1043	0.0000	1.0000
HKY	39	-1404.7277	2887.4554	0.0000	1.0000
SYM	40	-1409.7285	2899.4570	0.0000	1.0000
K2P	36	-1418.4971	2908.9943	0.0000	1.0000
F81G	39	-1433.8401	2945.6803	0.0000	1.0000
F81I	39	-1434.6044	2947.2088	0.0000	1.0000
F81IG	40	-1434.6046	2949.2091	0.0000	1.0000
JC69I	36	-1445.3807	2962.7613	0.0000	1.0000
JC69G	36	-1445.8994	2963.7988	0.0000	1.0000
JC69IG	37	-1445.3765	2964.7531	0.0000	1.0000
F81	38	-1449.6927	2975.3853	0.0000	1.0000
JC69	35	-1461.8066	2993.6133	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1386.6304	3034.1446	0.4916	0.4916
HKYI	40	-1386.8555	3034.5947	0.3926	0.8842
K2PI	37	-1398.7101	3038.7377	0.0495	0.9337
GTRG	44	-1376.5639	3040.0998	0.0250	0.9587
HKYIG	41	-1386.8559	3041.1175	0.0150	0.9737
GTRI	44	-1377.1310	3041.2340	0.0142	0.9879
K2PG	37	-1400.4437	3042.2049	0.0087	0.9967
K2PIG	38	-1398.7101	3045.2596	0.0019	0.9986
SYMI	41	-1389.9696	3047.3449	0.0007	0.9992
GTRIG	45	-1377.1310	3047.7562	0.0005	0.9998
SYMG	41	-1391.2416	3049.8890	0.0002	1.0000
SYMIG	42	-1389.9696	3053.8670	0.0000	1.0000
HKY	39	-1404.7277	3063.8170	0.0000	1.0000
GTR	43	-1395.0521	3070.5543	0.0000	1.0000
K2P	36	-1418.4971	3071.7896	0.0000	1.0000
SYM	40	-1409.7285	3080.3407	0.0000	1.0000
F81G	39	-1433.8401	3122.0419	0.0000	1.0000
F81I	39	-1434.6044	3123.5704	0.0000	1.0000
JC69I	36	-1445.3807	3125.5567	0.0000	1.0000
JC69G	36	-1445.8994	3126.5942	0.0000	1.0000
F81IG	40	-1434.6046	3130.0928	0.0000	1.0000
JC69IG	37	-1445.3765	3132.0705	0.0000	1.0000
F81	38	-1449.6927	3147.2249	0.0000	1.0000
JC69	35	-1461.8066	3151.8865	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/chr7_6276.phylip = 1 - 680;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6276.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/chr7_6276.phylip = 1 - 680;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6276.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/chr7_6276.phylip = 1 - 680;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6276.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

