
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:34 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/chr1_5522.phylip" (19 taxa, 896 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	-3400.1549	6892.9632	0.5156	0.5156
HKYG	40	-3404.9579	6893.7522	0.3475	0.8632
HKYIG	41	-3404.8232	6895.6793	0.1326	0.9958
GTRI	44	-3405.7911	6904.2356	0.0018	0.9976
GTRIG	45	-3404.9221	6904.7148	0.0014	0.9991
HKYI	40	-3410.8790	6905.5943	0.0009	1.0000
K2PG	37	-3447.9376	6973.1525	0.0000	1.0000
K2PIG	38	-3447.6572	6974.7729	0.0000	1.0000
SYMG	41	-3446.5228	6979.0784	0.0000	1.0000
GTR	43	-3445.7674	6981.9761	0.0000	1.0000
HKY	39	-3450.5446	6982.7340	0.0000	1.0000
K2PI	37	-3452.7670	6982.8114	0.0000	1.0000
SYMI	41	-3451.4720	6988.9767	0.0000	1.0000
SYMIG	42	-3450.5520	6989.3384	0.0000	1.0000
K2P	36	-3495.9382	7066.9778	0.0000	1.0000
SYM	40	-3495.2084	7074.2531	0.0000	1.0000
F81G	39	-3504.5803	7090.8054	0.0000	1.0000
F81I	39	-3505.1037	7091.8523	0.0000	1.0000
F81IG	40	-3504.3105	7092.4572	0.0000	1.0000
JC69G	36	-3542.6886	7160.4784	0.0000	1.0000
F81	38	-3541.0325	7161.5235	0.0000	1.0000
JC69I	36	-3543.3948	7161.8909	0.0000	1.0000
JC69IG	37	-3544.0498	7165.3769	0.0000	1.0000
JC69	35	-3580.8987	7234.7277	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3400.1549	6888.3098	0.6081	0.6081
HKYG	40	-3404.9579	6889.9159	0.2724	0.8805
HKYIG	41	-3404.8232	6891.6465	0.1147	0.9952
GTRI	44	-3405.7911	6899.5822	0.0022	0.9974
GTRIG	45	-3404.9221	6899.8443	0.0019	0.9993
HKYI	40	-3410.8790	6901.7580	0.0007	1.0000
K2PG	37	-3447.9376	6969.8751	0.0000	1.0000
K2PIG	38	-3447.6572	6971.3143	0.0000	1.0000
SYMG	41	-3446.5228	6975.0456	0.0000	1.0000
GTR	43	-3445.7674	6977.5348	0.0000	1.0000
HKY	39	-3450.5446	6979.0892	0.0000	1.0000
K2PI	37	-3452.7670	6979.5340	0.0000	1.0000
SYMI	41	-3451.4720	6984.9439	0.0000	1.0000
SYMIG	42	-3450.5520	6985.1039	0.0000	1.0000
K2P	36	-3495.9382	7063.8765	0.0000	1.0000
SYM	40	-3495.2084	7070.4168	0.0000	1.0000
F81G	39	-3504.5803	7087.1605	0.0000	1.0000
F81I	39	-3505.1037	7088.2075	0.0000	1.0000
F81IG	40	-3504.3105	7088.6209	0.0000	1.0000
JC69G	36	-3542.6886	7157.3771	0.0000	1.0000
F81	38	-3541.0325	7158.0649	0.0000	1.0000
JC69I	36	-3543.3948	7158.7896	0.0000	1.0000
JC69IG	37	-3544.0498	7162.0995	0.0000	1.0000
JC69	35	-3580.8987	7231.7975	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3404.9579	7081.8335	0.9606	0.9606
HKYIG	41	-3404.8232	7088.3621	0.0367	0.9973
HKYI	40	-3410.8790	7093.6757	0.0026	0.9999
GTRG	44	-3400.1549	7099.4192	0.0001	1.0000
GTRI	44	-3405.7911	7110.6916	0.0000	1.0000
GTRIG	45	-3404.9221	7115.7516	0.0000	1.0000
K2PG	37	-3447.9376	7147.3989	0.0000	1.0000
K2PIG	38	-3447.6572	7153.6361	0.0000	1.0000
K2PI	37	-3452.7670	7157.0578	0.0000	1.0000
HKY	39	-3450.5446	7166.2089	0.0000	1.0000
SYMG	41	-3446.5228	7171.7612	0.0000	1.0000
SYMI	41	-3451.4720	7181.6595	0.0000	1.0000
GTR	43	-3445.7674	7183.8463	0.0000	1.0000
SYMIG	42	-3450.5520	7186.6174	0.0000	1.0000
K2P	36	-3495.9382	7236.6023	0.0000	1.0000
SYM	40	-3495.2084	7262.3345	0.0000	1.0000
F81G	39	-3504.5803	7274.2802	0.0000	1.0000
F81I	39	-3505.1037	7275.3272	0.0000	1.0000
F81IG	40	-3504.3105	7280.5385	0.0000	1.0000
JC69G	36	-3542.6886	7330.1030	0.0000	1.0000
JC69I	36	-3543.3948	7331.5155	0.0000	1.0000
JC69IG	37	-3544.0498	7339.6233	0.0000	1.0000
F81	38	-3541.0325	7340.3866	0.0000	1.0000
JC69	35	-3580.8987	7399.7254	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/chr1_5522.phylip = 1 - 896;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5522.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/chr1_5522.phylip = 1 - 896;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5522.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/chr1_5522.phylip = 1 - 896;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5522.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

