
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:57 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_8793.phylip" (19 taxa, 992 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
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
HKYIG	41	-4539.4052	9164.4356	0.4148	0.4148
GTRIG	45	-4535.6162	9165.6088	0.2307	0.6455
HKYG	40	-4541.1061	9165.6613	0.2247	0.8702
GTRG	44	-4537.3392	9166.8601	0.1234	0.9936
HKYI	40	-4545.1716	9173.7922	0.0039	0.9974
GTRI	44	-4541.2150	9174.6116	0.0026	1.0000
SYMG	41	-4610.6143	9306.8538	0.0000	1.0000
SYMIG	42	-4615.7354	9319.2769	0.0000	1.0000
HKY	39	-4623.0261	9327.3296	0.0000	1.0000
GTR	43	-4619.4017	9328.7949	0.0000	1.0000
SYMI	41	-4621.7778	9329.1809	0.0000	1.0000
K2PIG	38	-4628.7353	9336.5808	0.0000	1.0000
K2PG	37	-4630.3484	9337.6444	0.0000	1.0000
F81IG	40	-4628.9195	9341.2880	0.0000	1.0000
F81G	39	-4630.3846	9342.0465	0.0000	1.0000
F81I	39	-4632.6142	9346.5058	0.0000	1.0000
K2PI	37	-4639.7536	9356.4548	0.0000	1.0000
F81	38	-4700.6564	9480.4230	0.0000	1.0000
SYM	40	-4701.7262	9486.9015	0.0000	1.0000
JC69IG	37	-4708.1956	9493.3387	0.0000	1.0000
JC69G	36	-4710.1937	9495.1769	0.0000	1.0000
JC69I	36	-4710.9162	9496.6220	0.0000	1.0000
K2P	36	-4717.0675	9508.9245	0.0000	1.0000
JC69	35	-4779.8373	9632.3106	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-4539.4052	9160.8104	0.3683	0.3683
GTRIG	45	-4535.6162	9161.2325	0.2982	0.6665
HKYG	40	-4541.1061	9162.2123	0.1827	0.8492
GTRG	44	-4537.3392	9162.6785	0.1447	0.9939
HKYI	40	-4545.1716	9170.3432	0.0031	0.9970
GTRI	44	-4541.2150	9170.4300	0.0030	1.0000
SYMG	41	-4610.6143	9303.2285	0.0000	1.0000
SYMIG	42	-4615.7354	9315.4708	0.0000	1.0000
HKY	39	-4623.0261	9324.0522	0.0000	1.0000
GTR	43	-4619.4017	9324.8033	0.0000	1.0000
SYMI	41	-4621.7778	9325.5557	0.0000	1.0000
K2PIG	38	-4628.7353	9333.4706	0.0000	1.0000
K2PG	37	-4630.3484	9334.6968	0.0000	1.0000
F81IG	40	-4628.9195	9337.8390	0.0000	1.0000
F81G	39	-4630.3846	9338.7692	0.0000	1.0000
F81I	39	-4632.6142	9343.2285	0.0000	1.0000
K2PI	37	-4639.7536	9353.5072	0.0000	1.0000
F81	38	-4700.6564	9477.3128	0.0000	1.0000
SYM	40	-4701.7262	9483.4525	0.0000	1.0000
JC69IG	37	-4708.1956	9490.3911	0.0000	1.0000
JC69G	36	-4710.1937	9492.3874	0.0000	1.0000
JC69I	36	-4710.9162	9493.8325	0.0000	1.0000
K2P	36	-4717.0675	9506.1350	0.0000	1.0000
JC69	35	-4779.8373	9629.6746	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4541.1061	9358.2012	0.8395	0.8395
HKYIG	41	-4539.4052	9361.6990	0.1460	0.9856
HKYI	40	-4545.1716	9366.3321	0.0144	1.0000
GTRG	44	-4537.3392	9378.2663	0.0000	1.0000
GTRIG	45	-4535.6162	9381.7200	0.0000	1.0000
GTRI	44	-4541.2150	9386.0178	0.0000	1.0000
SYMG	41	-4610.6143	9504.1172	0.0000	1.0000
HKY	39	-4623.0261	9515.1414	0.0000	1.0000
K2PG	37	-4630.3484	9515.9866	0.0000	1.0000
K2PIG	38	-4628.7353	9519.6601	0.0000	1.0000
SYMIG	42	-4615.7354	9521.2592	0.0000	1.0000
SYMI	41	-4621.7778	9526.4443	0.0000	1.0000
F81G	39	-4630.3846	9529.8584	0.0000	1.0000
F81IG	40	-4628.9195	9533.8279	0.0000	1.0000
F81I	39	-4632.6142	9534.3177	0.0000	1.0000
K2PI	37	-4639.7536	9534.7969	0.0000	1.0000
GTR	43	-4619.4017	9535.4914	0.0000	1.0000
F81	38	-4700.6564	9663.5023	0.0000	1.0000
JC69G	36	-4710.1937	9668.7774	0.0000	1.0000
JC69I	36	-4710.9162	9670.2225	0.0000	1.0000
JC69IG	37	-4708.1956	9671.6809	0.0000	1.0000
SYM	40	-4701.7262	9679.4414	0.0000	1.0000
K2P	36	-4717.0675	9682.5250	0.0000	1.0000
JC69	35	-4779.8373	9801.1649	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_8793.phylip = 1 - 992;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_8793.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_8793.phylip = 1 - 992;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_8793.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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_8793.phylip = 1 - 992;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_8793.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

