
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:35 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_11660.phylip" (19 taxa, 510 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	-1859.2598	3815.0357	0.4971	0.4971
HKYG	40	-1864.7682	3816.5300	0.2355	0.7326
GTRIG	45	-1859.1244	3817.1712	0.1709	0.9035
HKYIG	41	-1864.6216	3818.6023	0.0836	0.9871
GTRI	44	-1863.4420	3823.4001	0.0076	0.9947
HKYI	40	-1868.5532	3824.1001	0.0053	1.0000
K2PG	37	-1882.6423	3845.2421	0.0000	1.0000
K2PIG	38	-1882.4699	3847.2328	0.0000	1.0000
SYMG	41	-1880.0228	3849.4046	0.0000	1.0000
SYMIG	42	-1879.8769	3851.4882	0.0000	1.0000
K2PI	37	-1886.1711	3852.2999	0.0000	1.0000
SYMI	41	-1883.7606	3856.8803	0.0000	1.0000
GTR	43	-1886.8454	3867.8109	0.0000	1.0000
HKY	39	-1892.6772	3869.9926	0.0000	1.0000
K2P	36	-1911.6076	3900.8474	0.0000	1.0000
SYM	40	-1907.9385	3902.8705	0.0000	1.0000
F81G	39	-1918.3290	3921.2963	0.0000	1.0000
F81IG	40	-1918.1686	3923.3308	0.0000	1.0000
F81I	39	-1921.8769	3928.3920	0.0000	1.0000
JC69G	36	-1932.3539	3942.3400	0.0000	1.0000
JC69IG	37	-1932.1917	3944.3411	0.0000	1.0000
JC69I	36	-1935.8165	3949.2651	0.0000	1.0000
F81	38	-1945.8925	3974.0780	0.0000	1.0000
JC69	35	-1960.3059	3995.9282	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1859.2598	3806.5196	0.5691	0.5691
GTRIG	45	-1859.1244	3808.2488	0.2397	0.8089
HKYG	40	-1864.7682	3809.5364	0.1259	0.9348
HKYIG	41	-1864.6216	3811.2433	0.0536	0.9885
GTRI	44	-1863.4420	3814.8840	0.0087	0.9971
HKYI	40	-1868.5532	3817.1065	0.0029	1.0000
K2PG	37	-1882.6423	3839.2845	0.0000	1.0000
K2PIG	38	-1882.4699	3840.9398	0.0000	1.0000
SYMG	41	-1880.0228	3842.0456	0.0000	1.0000
SYMIG	42	-1879.8769	3843.7537	0.0000	1.0000
K2PI	37	-1886.1711	3846.3423	0.0000	1.0000
SYMI	41	-1883.7606	3849.5213	0.0000	1.0000
GTR	43	-1886.8454	3859.6907	0.0000	1.0000
HKY	39	-1892.6772	3863.3543	0.0000	1.0000
K2P	36	-1911.6076	3895.2153	0.0000	1.0000
SYM	40	-1907.9385	3895.8769	0.0000	1.0000
F81G	39	-1918.3290	3914.6580	0.0000	1.0000
F81IG	40	-1918.1686	3916.3372	0.0000	1.0000
F81I	39	-1921.8769	3921.7537	0.0000	1.0000
JC69G	36	-1932.3539	3936.7079	0.0000	1.0000
JC69IG	37	-1932.1917	3938.3835	0.0000	1.0000
JC69I	36	-1935.8165	3943.6330	0.0000	1.0000
F81	38	-1945.8925	3967.7850	0.0000	1.0000
JC69	35	-1960.3059	3990.6117	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1864.7682	3978.9128	0.9301	0.9301
HKYIG	41	-1864.6216	3984.8541	0.0477	0.9777
HKYI	40	-1868.5532	3986.4829	0.0211	0.9989
GTRG	44	-1859.2598	3992.8337	0.0009	0.9997
K2PG	37	-1882.6423	3995.9577	0.0002	0.9999
GTRIG	45	-1859.1244	3998.7973	0.0000	1.0000
GTRI	44	-1863.4420	4001.1981	0.0000	1.0000
K2PIG	38	-1882.4699	4001.8474	0.0000	1.0000
K2PI	37	-1886.1711	4003.0155	0.0000	1.0000
SYMG	41	-1880.0228	4015.6564	0.0000	1.0000
SYMIG	42	-1879.8769	4021.5990	0.0000	1.0000
SYMI	41	-1883.7606	4023.1321	0.0000	1.0000
HKY	39	-1892.6772	4028.4964	0.0000	1.0000
GTR	43	-1886.8454	4041.7704	0.0000	1.0000
K2P	36	-1911.6076	4047.6541	0.0000	1.0000
SYM	40	-1907.9385	4065.2533	0.0000	1.0000
F81G	39	-1918.3290	4079.8000	0.0000	1.0000
F81IG	40	-1918.1686	4085.7136	0.0000	1.0000
F81I	39	-1921.8769	4086.8957	0.0000	1.0000
JC69G	36	-1932.3539	4089.1467	0.0000	1.0000
JC69IG	37	-1932.1917	4095.0567	0.0000	1.0000
JC69I	36	-1935.8165	4096.0718	0.0000	1.0000
F81	38	-1945.8925	4128.6926	0.0000	1.0000
JC69	35	-1960.3059	4138.8161	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/chr5_11660.phylip = 1 - 510;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11660.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/chr5_11660.phylip = 1 - 510;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11660.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/chr5_11660.phylip = 1 - 510;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11660.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

