
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:33 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/chr5_2015.phylip" (19 taxa, 1246 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	-4648.7102	9388.7177	0.6622	0.6622
GTRIG	45	-4648.3109	9390.0719	0.3364	0.9986
HKYG	40	-4659.9441	9402.6102	0.0006	0.9992
GTRI	44	-4656.0514	9403.4001	0.0004	0.9997
HKYIG	41	-4659.5560	9403.9724	0.0003	1.0000
HKYI	40	-4666.8269	9416.3757	0.0000	1.0000
GTR	43	-4724.6825	9538.5131	0.0000	1.0000
HKY	39	-4732.8966	9546.3803	0.0000	1.0000
SYMG	41	-4772.9455	9630.7515	0.0000	1.0000
SYMIG	42	-4772.5944	9632.1912	0.0000	1.0000
K2PG	37	-4778.8132	9633.9541	0.0000	1.0000
K2PIG	38	-4778.4365	9635.3286	0.0000	1.0000
SYMI	41	-4779.5609	9643.9823	0.0000	1.0000
K2PI	37	-4785.4694	9647.2666	0.0000	1.0000
F81G	39	-4810.5197	9701.6265	0.0000	1.0000
F81IG	40	-4810.2876	9703.2972	0.0000	1.0000
F81I	39	-4816.0758	9712.7387	0.0000	1.0000
SYM	40	-4844.9234	9772.5689	0.0000	1.0000
K2P	36	-4850.0742	9774.3518	0.0000	1.0000
F81	38	-4876.6296	9831.7149	0.0000	1.0000
JC69G	36	-4900.1615	9874.5266	0.0000	1.0000
JC69IG	37	-4899.9312	9876.1903	0.0000	1.0000
JC69I	36	-4906.0914	9886.3863	0.0000	1.0000
JC69	35	-4967.2252	10006.5330	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4648.7102	9385.4204	0.6451	0.6451
GTRIG	45	-4648.3109	9386.6219	0.3538	0.9989
HKYG	40	-4659.9441	9399.8882	0.0005	0.9993
GTRI	44	-4656.0514	9400.1029	0.0004	0.9997
HKYIG	41	-4659.5560	9401.1120	0.0003	1.0000
HKYI	40	-4666.8269	9413.6537	0.0000	1.0000
GTR	43	-4724.6825	9535.3650	0.0000	1.0000
HKY	39	-4732.8966	9543.7932	0.0000	1.0000
SYMG	41	-4772.9455	9627.8910	0.0000	1.0000
SYMIG	42	-4772.5944	9629.1887	0.0000	1.0000
K2PG	37	-4778.8132	9631.6263	0.0000	1.0000
K2PIG	38	-4778.4365	9632.8730	0.0000	1.0000
SYMI	41	-4779.5609	9641.1218	0.0000	1.0000
K2PI	37	-4785.4694	9644.9388	0.0000	1.0000
F81G	39	-4810.5197	9699.0394	0.0000	1.0000
F81IG	40	-4810.2876	9700.5752	0.0000	1.0000
F81I	39	-4816.0758	9710.1517	0.0000	1.0000
SYM	40	-4844.9234	9769.8469	0.0000	1.0000
K2P	36	-4850.0742	9772.1483	0.0000	1.0000
F81	38	-4876.6296	9829.2592	0.0000	1.0000
JC69G	36	-4900.1615	9872.3231	0.0000	1.0000
JC69IG	37	-4899.9312	9873.8625	0.0000	1.0000
JC69I	36	-4906.0914	9884.1828	0.0000	1.0000
JC69	35	-4967.2252	10004.4504	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4659.9441	9604.9959	0.9144	0.9144
GTRG	44	-4648.7102	9611.0390	0.0446	0.9590
HKYIG	41	-4659.5560	9611.3474	0.0382	0.9972
GTRIG	45	-4648.3109	9617.3681	0.0019	0.9990
HKYI	40	-4666.8269	9618.7615	0.0009	1.0000
GTRI	44	-4656.0514	9625.7214	0.0000	1.0000
HKY	39	-4732.8966	9743.7733	0.0000	1.0000
GTR	43	-4724.6825	9755.8558	0.0000	1.0000
K2PG	37	-4778.8132	9821.3510	0.0000	1.0000
K2PIG	38	-4778.4365	9827.7253	0.0000	1.0000
K2PI	37	-4785.4694	9834.6634	0.0000	1.0000
SYMG	41	-4772.9455	9838.1265	0.0000	1.0000
SYMIG	42	-4772.5944	9844.5519	0.0000	1.0000
SYMI	41	-4779.5609	9851.3573	0.0000	1.0000
F81G	39	-4810.5197	9899.0195	0.0000	1.0000
F81IG	40	-4810.2876	9905.6829	0.0000	1.0000
F81I	39	-4816.0758	9910.1317	0.0000	1.0000
K2P	36	-4850.0742	9956.7453	0.0000	1.0000
SYM	40	-4844.9234	9974.9546	0.0000	1.0000
F81	38	-4876.6296	10024.1116	0.0000	1.0000
JC69G	36	-4900.1615	10056.9201	0.0000	1.0000
JC69IG	37	-4899.9312	10063.5872	0.0000	1.0000
JC69I	36	-4906.0914	10068.7798	0.0000	1.0000
JC69	35	-4967.2252	10183.9196	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/chr5_2015.phylip = 1 - 1246;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2015.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/chr5_2015.phylip = 1 - 1246;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2015.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/chr5_2015.phylip = 1 - 1246;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2015.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

