
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:29 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/chr12_5895.phylip" (19 taxa, 815 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: GTRG


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	-3575.0489	7243.2407	0.6507	0.6507
GTRIG	45	-3574.5509	7244.4855	0.3492	1.0000
HKYG	40	-3590.1919	7264.6215	0.0000	1.0000
HKYIG	41	-3589.6319	7265.7191	0.0000	1.0000
SYMG	41	-3590.7493	7267.9539	0.0000	1.0000
SYMIG	42	-3590.2555	7269.1898	0.0000	1.0000
GTRI	44	-3588.2889	7269.7206	0.0000	1.0000
K2PG	37	-3601.0444	7279.7079	0.0000	1.0000
K2PIG	38	-3600.4435	7280.7065	0.0000	1.0000
SYMI	41	-3601.2775	7289.0104	0.0000	1.0000
HKYI	40	-3603.1942	7290.6261	0.0000	1.0000
K2PI	37	-3614.7895	7307.1980	0.0000	1.0000
GTR	43	-3686.5920	7464.0919	0.0000	1.0000
HKY	39	-3698.2132	7478.4523	0.0000	1.0000
SYM	40	-3698.6019	7481.4415	0.0000	1.0000
K2P	36	-3708.6909	7492.8059	0.0000	1.0000
F81IG	40	-3729.0833	7542.4044	0.0000	1.0000
F81G	39	-3731.1491	7544.3240	0.0000	1.0000
JC69IG	37	-3739.3371	7556.2932	0.0000	1.0000
JC69G	36	-3741.6003	7558.6248	0.0000	1.0000
F81I	39	-3740.2886	7562.6030	0.0000	1.0000
JC69I	36	-3750.5827	7576.5896	0.0000	1.0000
F81	38	-3828.7616	7737.3429	0.0000	1.0000
JC69	35	-3838.4605	7750.1560	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3575.0489	7238.0978	0.6229	0.6229
GTRIG	45	-3574.5509	7239.1019	0.3771	1.0000
HKYG	40	-3590.1919	7260.3838	0.0000	1.0000
HKYIG	41	-3589.6319	7261.2638	0.0000	1.0000
SYMG	41	-3590.7493	7263.4985	0.0000	1.0000
SYMIG	42	-3590.2555	7264.5111	0.0000	1.0000
GTRI	44	-3588.2889	7264.5778	0.0000	1.0000
K2PG	37	-3601.0444	7276.0889	0.0000	1.0000
K2PIG	38	-3600.4435	7276.8870	0.0000	1.0000
SYMI	41	-3601.2775	7284.5550	0.0000	1.0000
HKYI	40	-3603.1942	7286.3884	0.0000	1.0000
K2PI	37	-3614.7895	7303.5789	0.0000	1.0000
GTR	43	-3686.5920	7459.1840	0.0000	1.0000
HKY	39	-3698.2132	7474.4265	0.0000	1.0000
SYM	40	-3698.6019	7477.2038	0.0000	1.0000
K2P	36	-3708.6909	7489.3818	0.0000	1.0000
F81IG	40	-3729.0833	7538.1667	0.0000	1.0000
F81G	39	-3731.1491	7540.2982	0.0000	1.0000
JC69IG	37	-3739.3371	7552.6742	0.0000	1.0000
JC69G	36	-3741.6003	7555.2007	0.0000	1.0000
F81I	39	-3740.2886	7558.5772	0.0000	1.0000
JC69I	36	-3750.5827	7573.1655	0.0000	1.0000
F81	38	-3828.7616	7733.5233	0.0000	1.0000
JC69	35	-3838.4605	7746.9210	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-3575.0489	7445.0381	0.7504	0.7504
HKYG	40	-3590.1919	7448.5113	0.1322	0.8825
K2PG	37	-3601.0444	7450.1068	0.0595	0.9420
GTRIG	45	-3574.5509	7450.7453	0.0432	0.9853
HKYIG	41	-3589.6319	7454.0945	0.0081	0.9934
K2PIG	38	-3600.4435	7455.6081	0.0038	0.9972
SYMG	41	-3590.7493	7456.3292	0.0027	0.9998
SYMIG	42	-3590.2555	7462.0450	0.0002	1.0000
GTRI	44	-3588.2889	7471.5181	0.0000	1.0000
HKYI	40	-3603.1942	7474.5159	0.0000	1.0000
SYMI	41	-3601.2775	7477.3857	0.0000	1.0000
K2PI	37	-3614.7895	7477.5969	0.0000	1.0000
HKY	39	-3698.2132	7657.8508	0.0000	1.0000
K2P	36	-3708.6909	7658.6965	0.0000	1.0000
GTR	43	-3686.5920	7661.4210	0.0000	1.0000
SYM	40	-3698.6019	7665.3313	0.0000	1.0000
F81G	39	-3731.1491	7723.7226	0.0000	1.0000
JC69G	36	-3741.6003	7724.5155	0.0000	1.0000
F81IG	40	-3729.0833	7726.2942	0.0000	1.0000
JC69IG	37	-3739.3371	7726.6922	0.0000	1.0000
F81I	39	-3740.2886	7742.0016	0.0000	1.0000
JC69I	36	-3750.5827	7742.4803	0.0000	1.0000
JC69	35	-3838.4605	7911.5326	0.0000	1.0000
F81	38	-3828.7616	7912.2444	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/chr12_5895.phylip = 1 - 815;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5895.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/chr12_5895.phylip = 1 - 815;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5895.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5895.phylip = 1 - 815;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5895.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;


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End of Output

