
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:22 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/chrZ_11555.phylip" (19 taxa, 479 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	-1874.3260	3836.1405	0.6177	0.6177
HKYIG	41	-1874.3260	3838.5331	0.1867	0.8044
HKYI	40	-1875.9220	3839.3326	0.1252	0.9296
GTRG	44	-1872.0783	3841.2811	0.0473	0.9769
GTRIG	45	-1872.0784	3843.7180	0.0140	0.9908
GTRI	44	-1873.7894	3844.7033	0.0085	0.9994
HKY	39	-1882.5062	3850.1195	0.0006	0.9999
GTR	43	-1880.1783	3855.0554	0.0000	1.0000
K2PG	37	-1890.6348	3861.6461	0.0000	1.0000
K2PIG	38	-1890.6349	3864.0061	0.0000	1.0000
K2PI	37	-1892.2440	3864.8644	0.0000	1.0000
SYMG	41	-1890.3211	3870.5233	0.0000	1.0000
SYMIG	42	-1890.3211	3872.9267	0.0000	1.0000
SYMI	41	-1891.9848	3873.8505	0.0000	1.0000
K2P	36	-1899.8392	3877.7055	0.0000	1.0000
SYM	40	-1899.6156	3886.7198	0.0000	1.0000
F81G	39	-1930.0101	3945.1272	0.0000	1.0000
F81IG	40	-1930.0102	3947.5089	0.0000	1.0000
F81I	39	-1931.3015	3947.7100	0.0000	1.0000
F81	38	-1937.2800	3957.2964	0.0000	1.0000
JC69G	36	-1945.1032	3968.2336	0.0000	1.0000
JC69IG	37	-1945.1033	3970.5829	0.0000	1.0000
JC69I	36	-1946.3881	3970.8033	0.0000	1.0000
JC69	35	-1953.0161	3981.7207	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1874.3260	3828.6519	0.5435	0.5435
HKYIG	41	-1874.3260	3830.6521	0.1999	0.7434
HKYI	40	-1875.9220	3831.8440	0.1102	0.8536
GTRG	44	-1872.0783	3832.1567	0.0942	0.9478
GTRIG	45	-1872.0784	3834.1568	0.0347	0.9825
GTRI	44	-1873.7894	3835.5789	0.0170	0.9995
HKY	39	-1882.5062	3843.0124	0.0004	0.9999
GTR	43	-1880.1783	3846.3566	0.0001	1.0000
K2PG	37	-1890.6348	3855.2697	0.0000	1.0000
K2PIG	38	-1890.6349	3857.2698	0.0000	1.0000
K2PI	37	-1892.2440	3858.4880	0.0000	1.0000
SYMG	41	-1890.3211	3862.6423	0.0000	1.0000
SYMIG	42	-1890.3211	3864.6423	0.0000	1.0000
SYMI	41	-1891.9848	3865.9695	0.0000	1.0000
K2P	36	-1899.8392	3871.6784	0.0000	1.0000
SYM	40	-1899.6156	3879.2313	0.0000	1.0000
F81G	39	-1930.0101	3938.0202	0.0000	1.0000
F81IG	40	-1930.0102	3940.0203	0.0000	1.0000
F81I	39	-1931.3015	3940.6029	0.0000	1.0000
F81	38	-1937.2800	3950.5601	0.0000	1.0000
JC69G	36	-1945.1032	3962.2064	0.0000	1.0000
JC69IG	37	-1945.1033	3964.2065	0.0000	1.0000
JC69I	36	-1946.3881	3964.7762	0.0000	1.0000
JC69	35	-1953.0161	3976.0322	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1874.3260	3995.5200	0.7964	0.7964
HKYI	40	-1875.9220	3998.7120	0.1614	0.9578
HKYIG	41	-1874.3260	4001.6918	0.0364	0.9942
HKY	39	-1882.5062	4005.7087	0.0049	0.9991
K2PG	37	-1890.6348	4009.6226	0.0007	0.9998
K2PI	37	-1892.2440	4012.8409	0.0001	0.9999
GTRG	44	-1872.0783	4015.7115	0.0000	1.0000
K2PIG	38	-1890.6349	4015.7944	0.0000	1.0000
GTRI	44	-1873.7894	4019.1337	0.0000	1.0000
K2P	36	-1899.8392	4021.8596	0.0000	1.0000
GTRIG	45	-1872.0784	4021.8834	0.0000	1.0000
GTR	43	-1880.1783	4025.7397	0.0000	1.0000
SYMG	41	-1890.3211	4033.6820	0.0000	1.0000
SYMI	41	-1891.9848	4037.0092	0.0000	1.0000
SYMIG	42	-1890.3211	4039.8537	0.0000	1.0000
SYM	40	-1899.6156	4046.0993	0.0000	1.0000
F81G	39	-1930.0101	4100.7165	0.0000	1.0000
F81I	39	-1931.3015	4103.2993	0.0000	1.0000
F81IG	40	-1930.0102	4106.8883	0.0000	1.0000
F81	38	-1937.2800	4109.0847	0.0000	1.0000
JC69G	36	-1945.1032	4112.3876	0.0000	1.0000
JC69I	36	-1946.3881	4114.9574	0.0000	1.0000
JC69IG	37	-1945.1033	4118.5594	0.0000	1.0000
JC69	35	-1953.0161	4122.0417	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/chrZ_11555.phylip = 1 - 479;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11555.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/chrZ_11555.phylip = 1 - 479;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11555.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/chrZ_11555.phylip = 1 - 479;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11555.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

