
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:08 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_4728.phylip" (19 taxa, 405 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1406.3888	2911.7776	0.3080	0.3080
GTRIG	45	-1405.7659	2913.0638	0.1619	0.4700
SYMG	41	-1410.8565	2913.2006	0.1512	0.6212
HKYG	40	-1412.5716	2914.1542	0.0939	0.7151
SYMIG	42	-1410.1190	2914.2160	0.0910	0.8061
K2PG	37	-1416.5282	2914.7185	0.0708	0.8769
HKYIG	41	-1411.8537	2915.1950	0.0558	0.9327
GTRI	44	-1408.6680	2916.3361	0.0315	0.9642
SYMI	41	-1413.2608	2918.0092	0.0137	0.9779
K2PI	37	-1418.3699	2918.4018	0.0112	0.9891
HKYI	40	-1415.1249	2919.2607	0.0073	0.9964
K2PIG	38	-1418.2896	2920.6776	0.0036	1.0000
F81G	39	-1441.6866	2969.9212	0.0000	1.0000
F81I	39	-1443.0709	2972.6898	0.0000	1.0000
F81IG	40	-1441.9830	2972.9770	0.0000	1.0000
HKY	39	-1444.7024	2975.9527	0.0000	1.0000
GTR	43	-1440.1015	2976.6851	0.0000	1.0000
SYM	40	-1445.2158	2979.4426	0.0000	1.0000
JC69G	36	-1450.8112	2980.8615	0.0000	1.0000
K2P	36	-1451.2138	2981.6667	0.0000	1.0000
JC69IG	37	-1451.0093	2983.6807	0.0000	1.0000
JC69I	36	-1452.4047	2984.0485	0.0000	1.0000
F81	38	-1474.8364	3033.7711	0.0000	1.0000
JC69	35	-1483.5374	3043.9041	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1406.3888	2900.7776	0.4038	0.4038
GTRIG	45	-1405.7659	2901.5318	0.2770	0.6808
SYMG	41	-1410.8565	2903.7130	0.0931	0.7739
SYMIG	42	-1410.1190	2904.2381	0.0716	0.8455
HKYG	40	-1412.5716	2905.1433	0.0455	0.8910
GTRI	44	-1408.6680	2905.3361	0.0413	0.9323
HKYIG	41	-1411.8537	2905.7074	0.0343	0.9667
K2PG	37	-1416.5282	2907.0564	0.0175	0.9842
SYMI	41	-1413.2608	2908.5216	0.0084	0.9926
HKYI	40	-1415.1249	2910.2497	0.0035	0.9961
K2PI	37	-1418.3699	2910.7397	0.0028	0.9989
K2PIG	38	-1418.2896	2912.5792	0.0011	1.0000
F81G	39	-1441.6866	2961.3733	0.0000	1.0000
F81IG	40	-1441.9830	2963.9660	0.0000	1.0000
F81I	39	-1443.0709	2964.1418	0.0000	1.0000
GTR	43	-1440.1015	2966.2031	0.0000	1.0000
HKY	39	-1444.7024	2967.4047	0.0000	1.0000
SYM	40	-1445.2158	2970.4316	0.0000	1.0000
JC69G	36	-1450.8112	2973.6224	0.0000	1.0000
K2P	36	-1451.2138	2974.4275	0.0000	1.0000
JC69IG	37	-1451.0093	2976.0186	0.0000	1.0000
JC69I	36	-1452.4047	2976.8094	0.0000	1.0000
F81	38	-1474.8364	3025.6728	0.0000	1.0000
JC69	35	-1483.5374	3037.0749	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1416.5282	3055.2002	0.8498	0.8498
K2PI	37	-1418.3699	3058.8835	0.1347	0.9845
K2PIG	38	-1418.2896	3064.7269	0.0073	0.9918
HKYG	40	-1412.5716	3065.2987	0.0055	0.9972
SYMG	41	-1410.8565	3067.8723	0.0015	0.9987
HKYIG	41	-1411.8537	3069.8667	0.0006	0.9993
HKYI	40	-1415.1249	3070.4052	0.0004	0.9997
SYMIG	42	-1410.1190	3072.4013	0.0002	0.9998
SYMI	41	-1413.2608	3072.6810	0.0001	1.0000
GTRG	44	-1406.3888	3076.9487	0.0000	1.0000
GTRI	44	-1408.6680	3081.5071	0.0000	1.0000
GTRIG	45	-1405.7659	3081.7067	0.0000	1.0000
F81G	39	-1441.6866	3117.5249	0.0000	1.0000
JC69G	36	-1450.8112	3117.7623	0.0000	1.0000
K2P	36	-1451.2138	3118.5675	0.0000	1.0000
F81I	39	-1443.0709	3120.2934	0.0000	1.0000
JC69I	36	-1452.4047	3120.9493	0.0000	1.0000
HKY	39	-1444.7024	3123.5563	0.0000	1.0000
F81IG	40	-1441.9830	3124.1215	0.0000	1.0000
JC69IG	37	-1451.0093	3124.1624	0.0000	1.0000
SYM	40	-1445.2158	3130.5871	0.0000	1.0000
GTR	43	-1440.1015	3138.3702	0.0000	1.0000
JC69	35	-1483.5374	3177.2109	0.0000	1.0000
F81	38	-1474.8364	3177.8205	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_4728.phylip = 1 - 405;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4728.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_4728.phylip = 1 - 405;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4728.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4728.phylip = 1 - 405;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4728.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

