
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:01 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_2725.phylip" (19 taxa, 1006 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	-4386.5097	8865.1400	0.5350	0.5350
GTRIG	45	-4385.5546	8865.4216	0.4647	0.9997
HKYG	40	-4399.0429	8881.4847	0.0002	0.9999
HKYIG	41	-4398.3883	8882.3493	0.0001	1.0000
GTRI	44	-4395.7972	8883.7150	0.0000	1.0000
HKYI	40	-4408.8545	8901.1079	0.0000	1.0000
SYMG	41	-4411.5072	8908.5869	0.0000	1.0000
SYMIG	42	-4410.8282	8909.4072	0.0000	1.0000
K2PG	37	-4416.5424	8909.9898	0.0000	1.0000
K2PIG	38	-4415.9102	8910.8855	0.0000	1.0000
SYMI	41	-4423.1931	8931.9588	0.0000	1.0000
K2PI	37	-4428.5156	8933.9362	0.0000	1.0000
F81G	39	-4513.6008	9108.4315	0.0000	1.0000
F81IG	40	-4513.1878	9109.7745	0.0000	1.0000
GTR	43	-4513.3032	9116.5399	0.0000	1.0000
F81I	39	-4522.1947	9125.6192	0.0000	1.0000
JC69G	36	-4526.2868	9127.3229	0.0000	1.0000
JC69IG	37	-4525.8536	9128.6121	0.0000	1.0000
HKY	39	-4525.7082	9132.6462	0.0000	1.0000
JC69I	36	-4535.9855	9146.7201	0.0000	1.0000
SYM	40	-4537.5059	9158.4108	0.0000	1.0000
K2P	36	-4544.1892	9163.1277	0.0000	1.0000
F81	38	-4630.6996	9340.4643	0.0000	1.0000
JC69	35	-4643.7167	9360.0314	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4386.5097	8861.0193	0.5111	0.5111
GTRIG	45	-4385.5546	8861.1091	0.4887	0.9998
HKYG	40	-4399.0429	8878.0857	0.0001	0.9999
HKYIG	41	-4398.3883	8878.7766	0.0001	1.0000
GTRI	44	-4395.7972	8879.5943	0.0000	1.0000
HKYI	40	-4408.8545	8897.7090	0.0000	1.0000
SYMG	41	-4411.5072	8905.0143	0.0000	1.0000
SYMIG	42	-4410.8282	8905.6564	0.0000	1.0000
K2PG	37	-4416.5424	8907.0848	0.0000	1.0000
K2PIG	38	-4415.9102	8907.8203	0.0000	1.0000
SYMI	41	-4423.1931	8928.3861	0.0000	1.0000
K2PI	37	-4428.5156	8931.0312	0.0000	1.0000
F81G	39	-4513.6008	9105.2016	0.0000	1.0000
F81IG	40	-4513.1878	9106.3755	0.0000	1.0000
GTR	43	-4513.3032	9112.6065	0.0000	1.0000
F81I	39	-4522.1947	9122.3893	0.0000	1.0000
JC69G	36	-4526.2868	9124.5737	0.0000	1.0000
JC69IG	37	-4525.8536	9125.7071	0.0000	1.0000
HKY	39	-4525.7082	9129.4164	0.0000	1.0000
JC69I	36	-4535.9855	9143.9709	0.0000	1.0000
SYM	40	-4537.5059	9155.0118	0.0000	1.0000
K2P	36	-4544.1892	9160.3784	0.0000	1.0000
F81	38	-4630.6996	9337.3991	0.0000	1.0000
JC69	35	-4643.7167	9357.4335	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4399.0429	9074.6352	0.7363	0.7363
GTRG	44	-4386.5097	9077.2238	0.2018	0.9381
HKYIG	41	-4398.3883	9080.2399	0.0447	0.9828
GTRIG	45	-4385.5546	9082.2273	0.0165	0.9993
K2PG	37	-4416.5424	9088.8931	0.0006	0.9999
HKYI	40	-4408.8545	9094.2585	0.0000	0.9999
K2PIG	38	-4415.9102	9094.5424	0.0000	1.0000
GTRI	44	-4395.7972	9095.7987	0.0000	1.0000
SYMG	41	-4411.5072	9106.4776	0.0000	1.0000
SYMIG	42	-4410.8282	9112.0334	0.0000	1.0000
K2PI	37	-4428.5156	9112.8395	0.0000	1.0000
SYMI	41	-4423.1931	9129.8494	0.0000	1.0000
F81G	39	-4513.6008	9296.8374	0.0000	1.0000
JC69G	36	-4526.2868	9301.4682	0.0000	1.0000
F81IG	40	-4513.1878	9302.9250	0.0000	1.0000
JC69IG	37	-4525.8536	9307.5154	0.0000	1.0000
F81I	39	-4522.1947	9314.0251	0.0000	1.0000
JC69I	36	-4535.9855	9320.8654	0.0000	1.0000
HKY	39	-4525.7082	9321.0521	0.0000	1.0000
GTR	43	-4513.3032	9323.8972	0.0000	1.0000
K2P	36	-4544.1892	9337.2730	0.0000	1.0000
SYM	40	-4537.5059	9351.5613	0.0000	1.0000
F81	38	-4630.6996	9524.1212	0.0000	1.0000
JC69	35	-4643.7167	9529.4143	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_2725.phylip = 1 - 1006;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_2725.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_2725.phylip = 1 - 1006;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_2725.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_2725.phylip = 1 - 1006;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_2725.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;


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

