
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:12 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_491.phylip" (19 taxa, 657 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-1818.0823	3721.4892	0.4972	0.4972
GTRG	44	-1814.2483	3722.9671	0.2375	0.7346
HKYIG	41	-1818.0379	3723.6758	0.1666	0.9012
GTRIG	45	-1814.5575	3725.8908	0.0550	0.9563
HKYI	40	-1820.9444	3727.2134	0.0284	0.9847
GTRI	44	-1816.9903	3728.4512	0.0153	1.0000
HKY	39	-1832.1250	3747.3067	0.0000	1.0000
GTR	43	-1829.5182	3751.2093	0.0000	1.0000
F81G	39	-1851.5276	3786.1119	0.0000	1.0000
F81IG	40	-1851.4827	3788.2900	0.0000	1.0000
F81I	39	-1853.2422	3789.5410	0.0000	1.0000
K2PG	37	-1858.2806	3795.1041	0.0000	1.0000
K2PIG	38	-1858.1977	3797.1915	0.0000	1.0000
K2PI	37	-1860.0587	3798.6602	0.0000	1.0000
SYMG	41	-1856.6382	3800.8763	0.0000	1.0000
SYMIG	42	-1856.5667	3803.0162	0.0000	1.0000
SYMI	41	-1858.3546	3804.3091	0.0000	1.0000
F81	38	-1864.3757	3809.5476	0.0000	1.0000
K2P	36	-1871.6615	3819.6198	0.0000	1.0000
SYM	40	-1869.9332	3825.1911	0.0000	1.0000
JC69G	36	-1885.0640	3846.4248	0.0000	1.0000
JC69IG	37	-1884.9765	3848.4958	0.0000	1.0000
JC69I	36	-1889.3554	3855.0076	0.0000	1.0000
JC69	35	-1899.7257	3873.5094	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1818.0823	3716.1645	0.3888	0.3888
GTRG	44	-1814.2483	3716.4965	0.3293	0.7181
HKYIG	41	-1818.0379	3718.0758	0.1495	0.8676
GTRIG	45	-1814.5575	3719.1150	0.0889	0.9566
HKYI	40	-1820.9444	3721.8888	0.0222	0.9788
GTRI	44	-1816.9903	3721.9806	0.0212	1.0000
HKY	39	-1832.1250	3742.2500	0.0000	1.0000
GTR	43	-1829.5182	3745.0363	0.0000	1.0000
F81G	39	-1851.5276	3781.0551	0.0000	1.0000
F81IG	40	-1851.4827	3782.9653	0.0000	1.0000
F81I	39	-1853.2422	3784.4843	0.0000	1.0000
K2PG	37	-1858.2806	3790.5613	0.0000	1.0000
K2PIG	38	-1858.1977	3792.3954	0.0000	1.0000
K2PI	37	-1860.0587	3794.1174	0.0000	1.0000
SYMG	41	-1856.6382	3795.2763	0.0000	1.0000
SYMIG	42	-1856.5667	3797.1335	0.0000	1.0000
SYMI	41	-1858.3546	3798.7091	0.0000	1.0000
F81	38	-1864.3757	3804.7515	0.0000	1.0000
K2P	36	-1871.6615	3815.3231	0.0000	1.0000
SYM	40	-1869.9332	3819.8665	0.0000	1.0000
JC69G	36	-1885.0640	3842.1280	0.0000	1.0000
JC69IG	37	-1884.9765	3843.9530	0.0000	1.0000
JC69I	36	-1889.3554	3850.7108	0.0000	1.0000
JC69	35	-1899.7257	3869.4514	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1818.0823	3895.6719	0.9107	0.9107
HKYI	40	-1820.9444	3901.3961	0.0520	0.9627
HKYIG	41	-1818.0379	3902.0708	0.0371	0.9999
GTRG	44	-1814.2483	3913.9546	0.0001	1.0000
HKY	39	-1832.1250	3917.2697	0.0000	1.0000
GTRI	44	-1816.9903	3919.4387	0.0000	1.0000
GTRIG	45	-1814.5575	3921.0608	0.0000	1.0000
GTR	43	-1829.5182	3938.0068	0.0000	1.0000
F81G	39	-1851.5276	3956.0748	0.0000	1.0000
K2PG	37	-1858.2806	3956.6056	0.0000	1.0000
F81I	39	-1853.2422	3959.5040	0.0000	1.0000
K2PI	37	-1860.0587	3960.1617	0.0000	1.0000
F81IG	40	-1851.4827	3962.4727	0.0000	1.0000
K2PIG	38	-1858.1977	3962.9274	0.0000	1.0000
F81	38	-1864.3757	3975.2835	0.0000	1.0000
K2P	36	-1871.6615	3976.8797	0.0000	1.0000
SYMG	41	-1856.6382	3979.2714	0.0000	1.0000
SYMI	41	-1858.3546	3982.7042	0.0000	1.0000
SYMIG	42	-1856.5667	3985.6162	0.0000	1.0000
SYM	40	-1869.9332	3999.3738	0.0000	1.0000
JC69G	36	-1885.0640	4003.6847	0.0000	1.0000
JC69IG	37	-1884.9765	4009.9973	0.0000	1.0000
JC69I	36	-1889.3554	4012.2674	0.0000	1.0000
JC69	35	-1899.7257	4026.5203	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_491.phylip = 1 - 657;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_491.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_491.phylip = 1 - 657;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_491.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;


[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/chr3_491.phylip = 1 - 657;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_491.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;


-------------------------------------------------------------
End of Output

