
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:05 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/chr2_24728.phylip" (19 taxa, 483 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	-1872.3807	3832.1823	0.4305	0.4305
HKYI	40	-1872.9971	3833.4150	0.2324	0.6630
GTRG	44	-1868.6518	3834.3448	0.1460	0.8090
HKYIG	41	-1872.3806	3834.5706	0.1304	0.9394
GTRIG	45	-1868.6517	3836.7770	0.0433	0.9827
GTRI	44	-1871.3191	3839.6793	0.0101	0.9929
K2PG	37	-1880.5279	3841.3749	0.0043	0.9972
K2PIG	38	-1880.5269	3843.7295	0.0013	0.9985
K2PI	37	-1881.7595	3843.8380	0.0013	0.9998
SYMG	41	-1878.9114	3847.6323	0.0002	1.0000
SYMIG	42	-1881.9276	3856.0643	0.0000	1.0000
SYMI	41	-1884.2335	3858.2765	0.0000	1.0000
HKY	39	-1907.8536	3900.7501	0.0000	1.0000
GTR	43	-1905.0705	3904.7607	0.0000	1.0000
K2P	36	-1915.3000	3908.5730	0.0000	1.0000
F81G	39	-1913.3914	3911.8258	0.0000	1.0000
F81I	39	-1914.4663	3913.9755	0.0000	1.0000
F81IG	40	-1913.3911	3914.2031	0.0000	1.0000
SYM	40	-1913.6634	3914.7476	0.0000	1.0000
JC69G	36	-1919.6743	3917.3217	0.0000	1.0000
JC69IG	37	-1923.1183	3926.5557	0.0000	1.0000
JC69I	36	-1925.2994	3928.5719	0.0000	1.0000
F81	38	-1947.3416	3977.3589	0.0000	1.0000
JC69	35	-1959.6780	3994.9936	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1872.3807	3824.7614	0.3318	0.3318
GTRG	44	-1868.6518	3825.3037	0.2530	0.5848
HKYI	40	-1872.9971	3825.9942	0.1791	0.7639
HKYIG	41	-1872.3806	3826.7611	0.1221	0.8860
GTRIG	45	-1868.6517	3827.3033	0.0931	0.9790
GTRI	44	-1871.3191	3830.6382	0.0176	0.9966
K2PG	37	-1880.5279	3835.0558	0.0019	0.9985
K2PIG	38	-1880.5269	3837.0539	0.0007	0.9993
K2PI	37	-1881.7595	3837.5189	0.0006	0.9998
SYMG	41	-1878.9114	3839.8228	0.0002	1.0000
SYMIG	42	-1881.9276	3847.8552	0.0000	1.0000
SYMI	41	-1884.2335	3850.4669	0.0000	1.0000
HKY	39	-1907.8536	3893.7072	0.0000	1.0000
GTR	43	-1905.0705	3896.1411	0.0000	1.0000
K2P	36	-1915.3000	3902.5999	0.0000	1.0000
F81G	39	-1913.3914	3904.7829	0.0000	1.0000
F81IG	40	-1913.3911	3906.7823	0.0000	1.0000
F81I	39	-1914.4663	3906.9326	0.0000	1.0000
SYM	40	-1913.6634	3907.3268	0.0000	1.0000
JC69G	36	-1919.6743	3911.3486	0.0000	1.0000
JC69IG	37	-1923.1183	3920.2366	0.0000	1.0000
JC69I	36	-1925.2994	3922.5988	0.0000	1.0000
F81	38	-1947.3416	3970.6832	0.0000	1.0000
JC69	35	-1959.6780	3989.3560	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1880.5279	3989.7164	0.5396	0.5396
HKYG	40	-1872.3807	3991.9621	0.1756	0.7151
K2PI	37	-1881.7595	3992.1795	0.1575	0.8726
HKYI	40	-1872.9971	3993.1949	0.0948	0.9674
K2PIG	38	-1880.5269	3995.8945	0.0246	0.9920
HKYIG	41	-1872.3806	3998.1418	0.0080	1.0000
GTRG	44	-1868.6518	4009.2244	0.0000	1.0000
SYMG	41	-1878.9114	4011.2034	0.0000	1.0000
GTRI	44	-1871.3191	4014.5589	0.0000	1.0000
GTRIG	45	-1868.6517	4015.4040	0.0000	1.0000
SYMI	41	-1884.2335	4021.8476	0.0000	1.0000
SYMIG	42	-1881.9276	4023.4159	0.0000	1.0000
K2P	36	-1915.3000	4053.0805	0.0000	1.0000
HKY	39	-1907.8536	4056.7278	0.0000	1.0000
JC69G	36	-1919.6743	4061.8292	0.0000	1.0000
F81G	39	-1913.3914	4067.8035	0.0000	1.0000
F81I	39	-1914.4663	4069.9533	0.0000	1.0000
JC69I	36	-1925.2994	4073.0794	0.0000	1.0000
F81IG	40	-1913.3911	4073.9829	0.0000	1.0000
SYM	40	-1913.6634	4074.5275	0.0000	1.0000
JC69IG	37	-1923.1183	4074.8972	0.0000	1.0000
GTR	43	-1905.0705	4075.8818	0.0000	1.0000
F81	38	-1947.3416	4129.5239	0.0000	1.0000
JC69	35	-1959.6780	4135.6566	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/chr2_24728.phylip = 1 - 483;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24728.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/chr2_24728.phylip = 1 - 483;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24728.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/chr2_24728.phylip = 1 - 483;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24728.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

