
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:20 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_7819.phylip" (19 taxa, 747 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	-2876.9849	5847.6109	0.5999	0.5999
GTRIG	45	-2876.2685	5848.4429	0.3957	0.9956
GTRI	44	-2882.2647	5858.1703	0.0031	0.9987
HKYG	40	-2888.0934	5860.8327	0.0008	0.9995
HKYIG	41	-2887.4199	5861.7250	0.0005	1.0000
HKYI	40	-2893.4965	5871.6388	0.0000	1.0000
SYMG	41	-2903.0841	5893.0534	0.0000	1.0000
SYMIG	42	-2902.0179	5893.1666	0.0000	1.0000
SYMI	41	-2907.8184	5902.5219	0.0000	1.0000
K2PG	37	-2913.9533	5905.8727	0.0000	1.0000
K2PIG	38	-2912.9504	5906.0873	0.0000	1.0000
K2PI	37	-2918.3201	5914.6064	0.0000	1.0000
HKY	39	-2952.5370	5987.4870	0.0000	1.0000
GTR	43	-2949.0713	5989.5252	0.0000	1.0000
F81G	39	-2960.0968	6002.6067	0.0000	1.0000
F81IG	40	-2959.6998	6004.0455	0.0000	1.0000
F81I	39	-2962.9174	6008.2478	0.0000	1.0000
SYM	40	-2967.6577	6019.9614	0.0000	1.0000
K2P	36	-2977.9323	6031.6167	0.0000	1.0000
JC69G	36	-2989.2380	6054.2280	0.0000	1.0000
JC69IG	37	-2988.2746	6054.5154	0.0000	1.0000
JC69I	36	-2994.0003	6063.7526	0.0000	1.0000
F81	38	-3026.6339	6133.4541	0.0000	1.0000
JC69	35	-3054.8663	6183.2769	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2876.9849	5841.9699	0.5683	0.5683
GTRIG	45	-2876.2685	5842.5371	0.4280	0.9963
GTRI	44	-2882.2647	5852.5293	0.0029	0.9992
HKYG	40	-2888.0934	5856.1868	0.0005	0.9997
HKYIG	41	-2887.4199	5856.8399	0.0003	1.0000
HKYI	40	-2893.4965	5866.9929	0.0000	1.0000
SYMIG	42	-2902.0179	5888.0359	0.0000	1.0000
SYMG	41	-2903.0841	5888.1683	0.0000	1.0000
SYMI	41	-2907.8184	5897.6368	0.0000	1.0000
K2PIG	38	-2912.9504	5901.9009	0.0000	1.0000
K2PG	37	-2913.9533	5901.9066	0.0000	1.0000
K2PI	37	-2918.3201	5910.6402	0.0000	1.0000
HKY	39	-2952.5370	5983.0740	0.0000	1.0000
GTR	43	-2949.0713	5984.1426	0.0000	1.0000
F81G	39	-2960.0968	5998.1937	0.0000	1.0000
F81IG	40	-2959.6998	5999.3996	0.0000	1.0000
F81I	39	-2962.9174	6003.8348	0.0000	1.0000
SYM	40	-2967.6577	6015.3155	0.0000	1.0000
K2P	36	-2977.9323	6027.8646	0.0000	1.0000
JC69G	36	-2989.2380	6050.4759	0.0000	1.0000
JC69IG	37	-2988.2746	6050.5492	0.0000	1.0000
JC69I	36	-2994.0003	6060.0005	0.0000	1.0000
F81	38	-3026.6339	6129.2677	0.0000	1.0000
JC69	35	-3054.8663	6179.7326	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2888.0934	6040.8294	0.8296	0.8296
GTRG	44	-2876.9849	6045.0767	0.0992	0.9288
HKYIG	41	-2887.4199	6046.0986	0.0595	0.9883
GTRIG	45	-2876.2685	6050.2600	0.0074	0.9958
HKYI	40	-2893.4965	6051.6355	0.0037	0.9995
GTRI	44	-2882.2647	6055.6362	0.0005	1.0000
K2PG	37	-2913.9533	6072.7010	0.0000	1.0000
K2PIG	38	-2912.9504	6077.3114	0.0000	1.0000
SYMG	41	-2903.0841	6077.4269	0.0000	1.0000
K2PI	37	-2918.3201	6081.4347	0.0000	1.0000
SYMIG	42	-2902.0179	6081.9106	0.0000	1.0000
SYMI	41	-2907.8184	6086.8955	0.0000	1.0000
HKY	39	-2952.5370	6163.1005	0.0000	1.0000
F81G	39	-2960.0968	6178.2202	0.0000	1.0000
GTR	43	-2949.0713	6182.6334	0.0000	1.0000
F81I	39	-2962.9174	6183.8613	0.0000	1.0000
F81IG	40	-2959.6998	6184.0422	0.0000	1.0000
K2P	36	-2977.9323	6194.0429	0.0000	1.0000
SYM	40	-2967.6577	6199.9581	0.0000	1.0000
JC69G	36	-2989.2380	6216.6543	0.0000	1.0000
JC69IG	37	-2988.2746	6221.3437	0.0000	1.0000
JC69I	36	-2994.0003	6226.1789	0.0000	1.0000
F81	38	-3026.6339	6304.6782	0.0000	1.0000
JC69	35	-3054.8663	6341.2948	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/chrZ_7819.phylip = 1 - 747;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7819.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/chrZ_7819.phylip = 1 - 747;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7819.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/chrZ_7819.phylip = 1 - 747;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7819.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

