
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:14 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_28805.phylip" (19 taxa, 570 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	-2082.1216	4259.7861	0.4949	0.4949
HKYG	40	-2087.8406	4261.8817	0.1736	0.6685
GTRIG	45	-2082.1231	4262.1470	0.1520	0.8205
GTRI	44	-2084.0266	4263.5961	0.0737	0.8941
HKYIG	41	-2087.8266	4264.1758	0.0551	0.9493
HKYI	40	-2089.6627	4265.5258	0.0281	0.9773
K2PG	37	-2093.9203	4267.1263	0.0126	0.9899
K2PIG	38	-2093.9011	4269.3842	0.0041	0.9940
SYMG	41	-2090.8815	4270.2857	0.0026	0.9966
K2PI	37	-2095.7099	4270.7056	0.0021	0.9987
SYMIG	42	-2090.8733	4272.6004	0.0008	0.9995
SYMI	41	-2092.5935	4273.7098	0.0005	1.0000
F81G	39	-2107.6918	4299.2704	0.0000	1.0000
JC69G	36	-2112.0409	4301.0800	0.0000	1.0000
F81IG	40	-2107.6753	4301.5510	0.0000	1.0000
F81I	39	-2109.5002	4302.8873	0.0000	1.0000
JC69IG	37	-2112.2519	4303.7895	0.0000	1.0000
JC69I	36	-2114.1543	4305.3066	0.0000	1.0000
HKY	39	-2118.3727	4320.6323	0.0000	1.0000
GTR	43	-2114.1238	4321.4415	0.0000	1.0000
K2P	36	-2123.4615	4323.9212	0.0000	1.0000
SYM	40	-2120.5022	4327.2047	0.0000	1.0000
F81	38	-2137.5612	4356.7044	0.0000	1.0000
JC69	35	-2141.6998	4358.1187	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2082.1216	4252.2432	0.5528	0.5528
GTRIG	45	-2082.1231	4254.2463	0.2031	0.7559
HKYG	40	-2087.8406	4255.6813	0.0991	0.8550
GTRI	44	-2084.0266	4256.0533	0.0823	0.9373
HKYIG	41	-2087.8266	4257.6531	0.0370	0.9742
HKYI	40	-2089.6627	4259.3254	0.0160	0.9903
K2PG	37	-2093.9203	4261.8406	0.0046	0.9948
SYMG	41	-2090.8815	4263.7630	0.0017	0.9966
K2PIG	38	-2093.9011	4263.8023	0.0017	0.9983
K2PI	37	-2095.7099	4265.4199	0.0008	0.9990
SYMIG	42	-2090.8733	4265.7466	0.0006	0.9997
SYMI	41	-2092.5935	4267.1870	0.0003	1.0000
F81G	39	-2107.6918	4293.3836	0.0000	1.0000
F81IG	40	-2107.6753	4295.3506	0.0000	1.0000
JC69G	36	-2112.0409	4296.0818	0.0000	1.0000
F81I	39	-2109.5002	4297.0005	0.0000	1.0000
JC69IG	37	-2112.2519	4298.5038	0.0000	1.0000
JC69I	36	-2114.1543	4300.3085	0.0000	1.0000
GTR	43	-2114.1238	4314.2476	0.0000	1.0000
HKY	39	-2118.3727	4314.7455	0.0000	1.0000
K2P	36	-2123.4615	4318.9230	0.0000	1.0000
SYM	40	-2120.5022	4321.0043	0.0000	1.0000
F81	38	-2137.5612	4351.1224	0.0000	1.0000
JC69	35	-2141.6998	4353.3996	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2093.9203	4422.6291	0.8010	0.8010
K2PI	37	-2095.7099	4426.2084	0.1338	0.9347
K2PIG	38	-2093.9011	4428.9365	0.0342	0.9689
HKYG	40	-2087.8406	4429.5067	0.0257	0.9947
HKYI	40	-2089.6627	4433.1509	0.0042	0.9988
HKYIG	41	-2087.8266	4435.8242	0.0011	0.9999
SYMG	41	-2090.8815	4441.9341	0.0001	1.0000
GTRG	44	-2082.1216	4443.4512	0.0000	1.0000
SYMI	41	-2092.5935	4445.3581	0.0000	1.0000
GTRI	44	-2084.0266	4447.2613	0.0000	1.0000
SYMIG	42	-2090.8733	4448.2633	0.0000	1.0000
GTRIG	45	-2082.1231	4449.7999	0.0000	1.0000
JC69G	36	-2112.0409	4452.5247	0.0000	1.0000
JC69I	36	-2114.1543	4456.7514	0.0000	1.0000
JC69IG	37	-2112.2519	4459.2923	0.0000	1.0000
F81G	39	-2107.6918	4462.8634	0.0000	1.0000
F81I	39	-2109.5002	4466.4803	0.0000	1.0000
F81IG	40	-2107.6753	4469.1761	0.0000	1.0000
K2P	36	-2123.4615	4475.3659	0.0000	1.0000
HKY	39	-2118.3727	4484.2253	0.0000	1.0000
SYM	40	-2120.5022	4494.8298	0.0000	1.0000
GTR	43	-2114.1238	4501.1099	0.0000	1.0000
JC69	35	-2141.6998	4505.4968	0.0000	1.0000
F81	38	-2137.5612	4516.2566	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_28805.phylip = 1 - 570;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28805.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_28805.phylip = 1 - 570;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28805.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/chr1_28805.phylip = 1 - 570;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28805.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

