
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:06 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/chr9_6414.phylip" (19 taxa, 734 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-1899.1345	3883.0020	0.2649	0.2649
HKYI	40	-1899.2435	3883.2200	0.2376	0.5025
HKYIG	41	-1899.1399	3885.2568	0.0858	0.5883
SYMG	41	-1899.2522	3885.4812	0.0767	0.6650
SYMI	41	-1899.4241	3885.8252	0.0646	0.7296
K2PG	37	-1903.9676	3885.9754	0.0599	0.7895
K2PI	37	-1904.0676	3886.1754	0.0542	0.8437
GTRG	44	-1896.2748	3886.2970	0.0510	0.8947
GTRI	44	-1896.4346	3886.6167	0.0435	0.9382
SYMIG	42	-1899.2262	3887.6796	0.0256	0.9638
K2PIG	38	-1903.9752	3888.2151	0.0195	0.9833
GTRIG	45	-1896.2573	3888.5320	0.0167	1.0000
HKY	39	-1918.4074	3919.3106	0.0000	1.0000
SYM	40	-1918.1507	3921.0344	0.0000	1.0000
K2P	36	-1922.8163	3921.4547	0.0000	1.0000
GTR	43	-1915.3644	3922.2128	0.0000	1.0000
F81I	39	-1920.6265	3923.7487	0.0000	1.0000
F81G	39	-1920.8269	3924.1496	0.0000	1.0000
JC69I	36	-1925.1990	3926.2202	0.0000	1.0000
F81IG	40	-1920.8268	3926.3867	0.0000	1.0000
JC69G	36	-1925.4256	3926.6732	0.0000	1.0000
JC69IG	37	-1925.4254	3928.8911	0.0000	1.0000
F81	38	-1938.3848	3957.0343	0.0000	1.0000
JC69	35	-1942.6460	3958.9022	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1899.1345	3878.2690	0.2461	0.2461
HKYI	40	-1899.2435	3878.4869	0.2207	0.4668
HKYIG	41	-1899.1399	3880.2799	0.0900	0.5568
SYMG	41	-1899.2522	3880.5043	0.0805	0.6373
GTRG	44	-1896.2748	3880.5495	0.0787	0.7160
SYMI	41	-1899.4241	3880.8483	0.0678	0.7838
GTRI	44	-1896.4346	3880.8692	0.0671	0.8508
K2PG	37	-1903.9676	3881.9352	0.0394	0.8902
K2PI	37	-1904.0676	3882.1352	0.0356	0.9258
SYMIG	42	-1899.2262	3882.4524	0.0304	0.9562
GTRIG	45	-1896.2573	3882.5146	0.0295	0.9856
K2PIG	38	-1903.9752	3883.9504	0.0144	1.0000
HKY	39	-1918.4074	3914.8149	0.0000	1.0000
SYM	40	-1918.1507	3916.3014	0.0000	1.0000
GTR	43	-1915.3644	3916.7288	0.0000	1.0000
K2P	36	-1922.8163	3917.6326	0.0000	1.0000
F81I	39	-1920.6265	3919.2530	0.0000	1.0000
F81G	39	-1920.8269	3919.6539	0.0000	1.0000
F81IG	40	-1920.8268	3921.6537	0.0000	1.0000
JC69I	36	-1925.1990	3922.3981	0.0000	1.0000
JC69G	36	-1925.4256	3922.8511	0.0000	1.0000
JC69IG	37	-1925.4254	3924.8509	0.0000	1.0000
F81	38	-1938.3848	3952.7695	0.0000	1.0000
JC69	35	-1942.6460	3955.2919	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1903.9676	4052.0800	0.5118	0.5118
K2PI	37	-1904.0676	4052.2800	0.4631	0.9748
K2PIG	38	-1903.9752	4058.6937	0.0187	0.9936
HKYG	40	-1899.1345	4062.2094	0.0032	0.9968
HKYI	40	-1899.2435	4062.4273	0.0029	0.9997
HKYIG	41	-1899.1399	4068.8188	0.0001	0.9998
SYMG	41	-1899.2522	4069.0432	0.0001	0.9999
SYMI	41	-1899.4241	4069.3872	0.0001	1.0000
SYMIG	42	-1899.2262	4075.5897	0.0000	1.0000
GTRG	44	-1896.2748	4082.8839	0.0000	1.0000
K2P	36	-1922.8163	4083.1789	0.0000	1.0000
GTRI	44	-1896.4346	4083.2036	0.0000	1.0000
JC69I	36	-1925.1990	4087.9444	0.0000	1.0000
JC69G	36	-1925.4256	4088.3975	0.0000	1.0000
GTRIG	45	-1896.2573	4089.4475	0.0000	1.0000
HKY	39	-1918.4074	4094.1567	0.0000	1.0000
JC69IG	37	-1925.4254	4094.9957	0.0000	1.0000
F81I	39	-1920.6265	4098.5949	0.0000	1.0000
F81G	39	-1920.8269	4098.9958	0.0000	1.0000
SYM	40	-1918.1507	4100.2417	0.0000	1.0000
F81IG	40	-1920.8268	4105.5940	0.0000	1.0000
GTR	43	-1915.3644	4114.4646	0.0000	1.0000
JC69	35	-1942.6460	4116.2397	0.0000	1.0000
F81	38	-1938.3848	4127.5129	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/chr9_6414.phylip = 1 - 734;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6414.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/chr9_6414.phylip = 1 - 734;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6414.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6414.phylip = 1 - 734;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6414.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

