
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:09 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/chr8_5307.phylip" (19 taxa, 985 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	-4267.5652	8627.3431	0.7440	0.7440
GTRIG	45	-4267.5653	8629.5395	0.2481	0.9922
HKYG	40	-4276.7761	8637.0268	0.0059	0.9980
HKYIG	41	-4276.7760	8639.2042	0.0020	1.0000
GTRI	44	-4282.1015	8656.4158	0.0000	1.0000
HKYI	40	-4291.7624	8666.9993	0.0000	1.0000
K2PG	37	-4339.6668	8756.3030	0.0000	1.0000
SYMG	41	-4336.1851	8758.0224	0.0000	1.0000
GTR	43	-4334.2105	8758.4424	0.0000	1.0000
K2PIG	38	-4339.6651	8758.4633	0.0000	1.0000
SYMIG	42	-4336.1690	8760.1725	0.0000	1.0000
HKY	39	-4345.1770	8771.6555	0.0000	1.0000
SYMI	41	-4348.5630	8782.7782	0.0000	1.0000
K2PI	37	-4353.8563	8784.6819	0.0000	1.0000
F81G	39	-4408.1490	8897.5995	0.0000	1.0000
F81IG	40	-4408.1489	8899.7723	0.0000	1.0000
SYM	40	-4409.2548	8901.9842	0.0000	1.0000
K2P	36	-4413.9810	8902.7721	0.0000	1.0000
F81I	39	-4419.9523	8921.2061	0.0000	1.0000
JC69G	36	-4454.5281	8983.8664	0.0000	1.0000
JC69IG	37	-4454.5323	8986.0341	0.0000	1.0000
JC69I	36	-4466.3994	9007.6090	0.0000	1.0000
F81	38	-4472.2369	9023.6069	0.0000	1.0000
JC69	35	-4522.8477	9118.3509	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4267.5652	8623.1304	0.7271	0.7271
GTRIG	45	-4267.5653	8625.1306	0.2675	0.9946
HKYG	40	-4276.7761	8633.5522	0.0040	0.9985
HKYIG	41	-4276.7760	8635.5520	0.0015	1.0000
GTRI	44	-4282.1015	8652.2031	0.0000	1.0000
HKYI	40	-4291.7624	8663.5247	0.0000	1.0000
K2PG	37	-4339.6668	8753.3336	0.0000	1.0000
SYMG	41	-4336.1851	8754.3702	0.0000	1.0000
GTR	43	-4334.2105	8754.4211	0.0000	1.0000
K2PIG	38	-4339.6651	8755.3301	0.0000	1.0000
SYMIG	42	-4336.1690	8756.3381	0.0000	1.0000
HKY	39	-4345.1770	8768.3539	0.0000	1.0000
SYMI	41	-4348.5630	8779.1260	0.0000	1.0000
K2PI	37	-4353.8563	8781.7126	0.0000	1.0000
F81G	39	-4408.1490	8894.2979	0.0000	1.0000
F81IG	40	-4408.1489	8896.2977	0.0000	1.0000
SYM	40	-4409.2548	8898.5097	0.0000	1.0000
K2P	36	-4413.9810	8899.9619	0.0000	1.0000
F81I	39	-4419.9523	8917.9045	0.0000	1.0000
JC69G	36	-4454.5281	8981.0563	0.0000	1.0000
JC69IG	37	-4454.5323	8983.0647	0.0000	1.0000
JC69I	36	-4466.3994	9004.7989	0.0000	1.0000
F81	38	-4472.2369	9020.4737	0.0000	1.0000
JC69	35	-4522.8477	9115.6954	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4276.7761	8829.2579	0.9592	0.9592
HKYIG	41	-4276.7760	8836.1503	0.0306	0.9898
GTRG	44	-4267.5652	8838.4066	0.0099	0.9997
GTRIG	45	-4267.5653	8845.2995	0.0003	1.0000
HKYI	40	-4291.7624	8859.2304	0.0000	1.0000
GTRI	44	-4282.1015	8867.4793	0.0000	1.0000
K2PG	37	-4339.6668	8934.3613	0.0000	1.0000
K2PIG	38	-4339.6651	8941.2505	0.0000	1.0000
SYMG	41	-4336.1851	8954.9685	0.0000	1.0000
HKY	39	-4345.1770	8959.1670	0.0000	1.0000
SYMIG	42	-4336.1690	8961.8290	0.0000	1.0000
K2PI	37	-4353.8563	8962.7403	0.0000	1.0000
GTR	43	-4334.2105	8964.8047	0.0000	1.0000
SYMI	41	-4348.5630	8979.7243	0.0000	1.0000
K2P	36	-4413.9810	9076.0970	0.0000	1.0000
F81G	39	-4408.1490	9085.1110	0.0000	1.0000
F81IG	40	-4408.1489	9092.0034	0.0000	1.0000
SYM	40	-4409.2548	9094.2153	0.0000	1.0000
F81I	39	-4419.9523	9108.7176	0.0000	1.0000
JC69G	36	-4454.5281	9157.1914	0.0000	1.0000
JC69IG	37	-4454.5323	9164.0924	0.0000	1.0000
JC69I	36	-4466.3994	9180.9340	0.0000	1.0000
F81	38	-4472.2369	9206.3941	0.0000	1.0000
JC69	35	-4522.8477	9286.9379	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/chr8_5307.phylip = 1 - 985;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_5307.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/chr8_5307.phylip = 1 - 985;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_5307.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/chr8_5307.phylip = 1 - 985;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_5307.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

