
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:22 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_1300.phylip" (19 taxa, 563 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1837.9534	3771.5516	0.4410	0.4410
GTRI	44	-1838.0649	3771.7746	0.3944	0.8354
GTRIG	45	-1837.8000	3773.6077	0.1577	0.9931
HKYG	40	-1847.7480	3781.7795	0.0027	0.9958
HKYI	40	-1847.9814	3782.2463	0.0021	0.9979
HKYIG	41	-1847.6569	3783.9241	0.0009	0.9988
SYMG	41	-1848.2808	3785.1720	0.0005	0.9993
SYMI	41	-1848.5139	3785.6381	0.0004	0.9997
SYMIG	42	-1848.2068	3787.3598	0.0002	0.9998
K2PG	37	-1854.5684	3788.4931	0.0001	0.9999
K2PI	37	-1855.0686	3789.4934	0.0001	1.0000
K2PIG	38	-1854.5192	3790.6948	0.0000	1.0000
GTR	43	-1855.5149	3804.3208	0.0000	1.0000
HKY	39	-1864.3145	3812.5946	0.0000	1.0000
SYM	40	-1864.3893	3815.0622	0.0000	1.0000
K2P	36	-1870.9982	3819.0610	0.0000	1.0000
F81G	39	-1893.4049	3870.7753	0.0000	1.0000
F81I	39	-1894.2739	3872.5134	0.0000	1.0000
F81IG	40	-1893.3696	3873.0227	0.0000	1.0000
JC69G	36	-1898.6739	3874.4124	0.0000	1.0000
JC69I	36	-1899.5652	3876.1951	0.0000	1.0000
JC69IG	37	-1898.6424	3876.6410	0.0000	1.0000
F81	38	-1909.6452	3900.9468	0.0000	1.0000
JC69	35	-1914.6224	3904.0266	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1837.9534	3763.9068	0.4289	0.4289
GTRI	44	-1838.0649	3764.1298	0.3836	0.8125
GTRIG	45	-1837.8000	3765.6000	0.1839	0.9965
HKYG	40	-1847.7480	3775.4960	0.0013	0.9978
HKYI	40	-1847.9814	3775.9628	0.0010	0.9988
HKYIG	41	-1847.6569	3777.3138	0.0005	0.9993
SYMG	41	-1848.2808	3778.5617	0.0003	0.9996
SYMI	41	-1848.5139	3779.0277	0.0002	0.9998
SYMIG	42	-1848.2068	3780.4136	0.0001	0.9999
K2PG	37	-1854.5684	3783.1369	0.0000	1.0000
K2PI	37	-1855.0686	3784.1372	0.0000	1.0000
K2PIG	38	-1854.5192	3785.0384	0.0000	1.0000
GTR	43	-1855.5149	3797.0298	0.0000	1.0000
HKY	39	-1864.3145	3806.6290	0.0000	1.0000
SYM	40	-1864.3893	3808.7787	0.0000	1.0000
K2P	36	-1870.9982	3813.9964	0.0000	1.0000
F81G	39	-1893.4049	3864.8098	0.0000	1.0000
F81I	39	-1894.2739	3866.5478	0.0000	1.0000
F81IG	40	-1893.3696	3866.7392	0.0000	1.0000
JC69G	36	-1898.6739	3869.3478	0.0000	1.0000
JC69I	36	-1899.5652	3871.1305	0.0000	1.0000
JC69IG	37	-1898.6424	3871.2848	0.0000	1.0000
F81	38	-1909.6452	3895.2903	0.0000	1.0000
JC69	35	-1914.6224	3899.2448	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1854.5684	3943.4682	0.5595	0.5595
K2PI	37	-1855.0686	3944.4686	0.3393	0.8987
HKYG	40	-1847.7480	3948.8272	0.0384	0.9371
HKYI	40	-1847.9814	3949.2940	0.0304	0.9675
K2PIG	38	-1854.5192	3949.7030	0.0248	0.9923
GTRG	44	-1837.9534	3954.5711	0.0022	0.9944
GTRI	44	-1838.0649	3954.7941	0.0019	0.9964
HKYIG	41	-1847.6569	3954.9782	0.0018	0.9981
SYMG	41	-1848.2808	3956.2261	0.0009	0.9991
SYMI	41	-1848.5139	3956.6922	0.0008	0.9998
GTRIG	45	-1837.8000	3960.5975	0.0001	1.0000
SYMIG	42	-1848.2068	3962.4114	0.0000	1.0000
K2P	36	-1870.9982	3969.9944	0.0000	1.0000
HKY	39	-1864.3145	3975.6269	0.0000	1.0000
SYM	40	-1864.3893	3982.1099	0.0000	1.0000
GTR	43	-1855.5149	3983.3609	0.0000	1.0000
JC69G	36	-1898.6739	4025.3458	0.0000	1.0000
JC69I	36	-1899.5652	4027.1285	0.0000	1.0000
JC69IG	37	-1898.6424	4031.6161	0.0000	1.0000
F81G	39	-1893.4049	4033.8077	0.0000	1.0000
F81I	39	-1894.2739	4035.5457	0.0000	1.0000
F81IG	40	-1893.3696	4040.0703	0.0000	1.0000
JC69	35	-1914.6224	4050.9096	0.0000	1.0000
F81	38	-1909.6452	4059.9549	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_1300.phylip = 1 - 563;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_1300.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/chr3_1300.phylip = 1 - 563;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_1300.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_1300.phylip = 1 - 563;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_1300.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

