
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
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_5587.phylip" (19 taxa, 389 characters)

Minimum AIC  model: GTRG
Minimum AICc model: K2PG
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
K2PG	37	-1504.8657	3091.7427	0.2910	0.2910
HKYG	40	-1501.5072	3092.4396	0.2054	0.4965
K2PI	37	-1505.8708	3093.7529	0.1065	0.6030
GTRG	44	-1497.2532	3094.0181	0.0933	0.6963
K2PIG	38	-1504.8658	3094.2002	0.0852	0.7814
HKYI	40	-1502.5158	3094.4569	0.0749	0.8564
HKYIG	41	-1501.5081	3094.9413	0.0588	0.9152
GTRI	44	-1498.4292	3096.3700	0.0288	0.9439
GTRIG	45	-1497.2529	3096.5758	0.0260	0.9699
SYMG	41	-1502.6749	3097.2749	0.0183	0.9882
SYMI	41	-1503.7249	3099.3748	0.0064	0.9946
SYMIG	42	-1502.6745	3099.7884	0.0052	0.9998
K2P	36	-1514.0751	3107.7185	0.0001	0.9999
HKY	39	-1511.1260	3109.1919	0.0000	1.0000
GTR	43	-1507.9597	3112.8875	0.0000	1.0000
SYM	40	-1512.0992	3113.6237	0.0000	1.0000
JC69G	36	-1540.2015	3159.9712	0.0000	1.0000
JC69I	36	-1540.9763	3161.5208	0.0000	1.0000
JC69IG	37	-1540.2125	3162.4364	0.0000	1.0000
F81G	39	-1538.3515	3163.6428	0.0000	1.0000
F81I	39	-1539.1217	3165.1832	0.0000	1.0000
F81IG	40	-1538.3529	3166.1311	0.0000	1.0000
JC69	35	-1548.0563	3173.2515	0.0000	1.0000
F81	38	-1546.3740	3177.2166	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1497.2532	3082.5065	0.2431	0.2431
HKYG	40	-1501.5072	3083.0143	0.1886	0.4317
K2PG	37	-1504.8657	3083.7313	0.1318	0.5635
GTRIG	45	-1497.2529	3084.5058	0.0895	0.6530
GTRI	44	-1498.4292	3084.8584	0.0750	0.7280
HKYIG	41	-1501.5081	3085.0163	0.0693	0.7973
HKYI	40	-1502.5158	3085.0316	0.0688	0.8661
K2PIG	38	-1504.8658	3085.7316	0.0485	0.9146
K2PI	37	-1505.8708	3085.7415	0.0482	0.9628
SYMG	41	-1502.6749	3087.3498	0.0216	0.9844
SYMIG	42	-1502.6745	3089.3491	0.0079	0.9924
SYMI	41	-1503.7249	3089.4497	0.0076	0.9999
K2P	36	-1514.0751	3100.1503	0.0000	0.9999
HKY	39	-1511.1260	3100.2521	0.0000	1.0000
GTR	43	-1507.9597	3101.9194	0.0000	1.0000
SYM	40	-1512.0992	3104.1985	0.0000	1.0000
JC69G	36	-1540.2015	3152.4030	0.0000	1.0000
JC69I	36	-1540.9763	3153.9527	0.0000	1.0000
JC69IG	37	-1540.2125	3154.4250	0.0000	1.0000
F81G	39	-1538.3515	3154.7030	0.0000	1.0000
F81I	39	-1539.1217	3156.2433	0.0000	1.0000
F81IG	40	-1538.3529	3156.7058	0.0000	1.0000
JC69	35	-1548.0563	3166.1126	0.0000	1.0000
F81	38	-1546.3740	3168.7480	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1504.8657	3230.3838	0.7022	0.7022
K2PI	37	-1505.8708	3232.3939	0.2570	0.9592
K2PIG	38	-1504.8658	3236.3477	0.0356	0.9948
HKYG	40	-1501.5072	3241.5575	0.0026	0.9975
K2P	36	-1514.0751	3242.8392	0.0014	0.9988
HKYI	40	-1502.5158	3243.5748	0.0010	0.9998
HKYIG	41	-1501.5081	3247.5230	0.0001	0.9999
SYMG	41	-1502.6749	3249.8566	0.0000	1.0000
SYMI	41	-1503.7249	3251.9565	0.0000	1.0000
HKY	39	-1511.1260	3254.8317	0.0000	1.0000
SYMIG	42	-1502.6745	3255.8194	0.0000	1.0000
GTRG	44	-1497.2532	3256.9040	0.0000	1.0000
GTRI	44	-1498.4292	3259.2559	0.0000	1.0000
SYM	40	-1512.0992	3262.7416	0.0000	1.0000
GTRIG	45	-1497.2529	3262.8669	0.0000	1.0000
GTR	43	-1507.9597	3272.3533	0.0000	1.0000
JC69G	36	-1540.2015	3295.0919	0.0000	1.0000
JC69I	36	-1540.9763	3296.6415	0.0000	1.0000
JC69IG	37	-1540.2125	3301.0775	0.0000	1.0000
JC69	35	-1548.0563	3304.8379	0.0000	1.0000
F81G	39	-1538.3515	3309.2826	0.0000	1.0000
F81I	39	-1539.1217	3310.8229	0.0000	1.0000
F81IG	40	-1538.3529	3315.2490	0.0000	1.0000
F81	38	-1546.3740	3319.3640	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_5587.phylip = 1 - 389;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5587.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5587.phylip = 1 - 389;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5587.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;


[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/chr3_5587.phylip = 1 - 389;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5587.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

