
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:49 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/chr7_6259.phylip" (19 taxa, 813 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: HKYI


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
GTRIG	45	-1870.8737	3837.1451	0.5355	0.5355
GTRI	44	-1872.7959	3838.7480	0.2403	0.7758
GTRG	44	-1872.8726	3838.9015	0.2225	0.9983
HKYI	40	-1883.2902	3850.8292	0.0006	0.9989
HKYG	40	-1883.3185	3850.8857	0.0006	0.9994
HKYIG	41	-1882.2380	3850.9429	0.0005	1.0000
SYMIG	42	-1885.7185	3860.1279	0.0000	1.0000
SYMG	41	-1887.4751	3861.4170	0.0000	1.0000
SYMI	41	-1888.8651	3864.1970	0.0000	1.0000
K2PG	37	-1893.9886	3865.6055	0.0000	1.0000
K2PI	37	-1894.0040	3865.6364	0.0000	1.0000
K2PIG	38	-1892.9592	3865.7478	0.0000	1.0000
GTR	43	-1901.1674	3893.2555	0.0000	1.0000
HKY	39	-1908.3103	3898.6568	0.0000	1.0000
SYM	40	-1913.4532	3911.1550	0.0000	1.0000
K2P	36	-1918.2756	3911.9841	0.0000	1.0000
F81G	39	-1929.7369	3941.5100	0.0000	1.0000
F81I	39	-1929.8124	3941.6611	0.0000	1.0000
F81IG	40	-1928.9522	3942.1530	0.0000	1.0000
JC69G	36	-1938.3779	3952.1888	0.0000	1.0000
JC69I	36	-1938.4610	3952.3551	0.0000	1.0000
JC69IG	37	-1937.5831	3952.7945	0.0000	1.0000
F81	38	-1952.9791	3985.7877	0.0000	1.0000
JC69	35	-1961.5163	3996.2758	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1870.8737	3831.7474	0.5657	0.5657
GTRI	44	-1872.7959	3833.5918	0.2249	0.7906
GTRG	44	-1872.8726	3833.7453	0.2083	0.9990
HKYIG	41	-1882.2380	3846.4760	0.0004	0.9993
HKYI	40	-1883.2902	3846.5805	0.0003	0.9997
HKYG	40	-1883.3185	3846.6370	0.0003	1.0000
SYMIG	42	-1885.7185	3855.4370	0.0000	1.0000
SYMG	41	-1887.4751	3856.9501	0.0000	1.0000
SYMI	41	-1888.8651	3859.7301	0.0000	1.0000
K2PIG	38	-1892.9592	3861.9184	0.0000	1.0000
K2PG	37	-1893.9886	3861.9771	0.0000	1.0000
K2PI	37	-1894.0040	3862.0080	0.0000	1.0000
GTR	43	-1901.1674	3888.3348	0.0000	1.0000
HKY	39	-1908.3103	3894.6206	0.0000	1.0000
SYM	40	-1913.4532	3906.9063	0.0000	1.0000
K2P	36	-1918.2756	3908.5512	0.0000	1.0000
F81G	39	-1929.7369	3937.4738	0.0000	1.0000
F81I	39	-1929.8124	3937.6248	0.0000	1.0000
F81IG	40	-1928.9522	3937.9043	0.0000	1.0000
JC69G	36	-1938.3779	3948.7558	0.0000	1.0000
JC69I	36	-1938.4610	3948.9221	0.0000	1.0000
JC69IG	37	-1937.5831	3949.1662	0.0000	1.0000
F81	38	-1952.9791	3981.9583	0.0000	1.0000
JC69	35	-1961.5163	3993.0326	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1883.2902	4034.6097	0.3047	0.3047
HKYG	40	-1883.3185	4034.6662	0.2962	0.6009
K2PG	37	-1893.9886	4035.9042	0.1595	0.7604
K2PI	37	-1894.0040	4035.9351	0.1571	0.9174
HKYIG	41	-1882.2380	4039.2059	0.0306	0.9481
GTRI	44	-1872.7959	4040.4239	0.0166	0.9647
K2PIG	38	-1892.9592	4040.5462	0.0157	0.9804
GTRG	44	-1872.8726	4040.5774	0.0154	0.9958
GTRIG	45	-1870.8737	4043.2803	0.0040	0.9998
SYMG	41	-1887.4751	4049.6801	0.0002	0.9999
SYMI	41	-1888.8651	4052.4601	0.0000	1.0000
SYMIG	42	-1885.7185	4052.8677	0.0000	1.0000
K2P	36	-1918.2756	4077.7775	0.0000	1.0000
HKY	39	-1908.3103	4077.9491	0.0000	1.0000
GTR	43	-1901.1674	4090.4662	0.0000	1.0000
SYM	40	-1913.4532	4094.9355	0.0000	1.0000
JC69G	36	-1938.3779	4117.9821	0.0000	1.0000
JC69I	36	-1938.4610	4118.1484	0.0000	1.0000
F81G	39	-1929.7369	4120.8023	0.0000	1.0000
F81I	39	-1929.8124	4120.9534	0.0000	1.0000
JC69IG	37	-1937.5831	4123.0932	0.0000	1.0000
F81IG	40	-1928.9522	4125.9336	0.0000	1.0000
JC69	35	-1961.5163	4157.5582	0.0000	1.0000
F81	38	-1952.9791	4160.5861	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6259.phylip = 1 - 813;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6259.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6259.phylip = 1 - 813;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6259.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6259.phylip = 1 - 813;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6259.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

