
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:25 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/chr1_14909.phylip" (19 taxa, 776 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-2867.3090	5819.0805	0.4813	0.4813
HKYIG	41	-2866.9848	5820.6618	0.2183	0.6995
GTRG	44	-2863.9088	5821.2347	0.1639	0.8634
GTRIG	45	-2863.6406	5822.9524	0.0694	0.9329
HKYI	40	-2869.5112	5823.4849	0.0532	0.9861
GTRI	44	-2866.3840	5826.1852	0.0138	0.9999
K2PG	37	-2879.4300	5836.6703	0.0001	0.9999
K2PIG	38	-2878.9629	5837.9474	0.0000	1.0000
K2PI	37	-2880.9020	5839.6143	0.0000	1.0000
SYMG	41	-2878.4045	5843.5011	0.0000	1.0000
SYMIG	42	-2877.8917	5844.7112	0.0000	1.0000
SYMI	41	-2879.5477	5845.7876	0.0000	1.0000
HKY	39	-2927.1782	5936.5955	0.0000	1.0000
GTR	43	-2924.1896	5939.5486	0.0000	1.0000
K2P	36	-2937.9620	5951.5289	0.0000	1.0000
SYM	40	-2936.2842	5957.0310	0.0000	1.0000
F81G	39	-2948.2597	5978.7586	0.0000	1.0000
F81IG	40	-2947.9641	5980.3908	0.0000	1.0000
F81I	39	-2949.9320	5982.1032	0.0000	1.0000
JC69G	36	-2956.6450	5988.8949	0.0000	1.0000
JC69IG	37	-2956.3041	5990.4186	0.0000	1.0000
JC69I	36	-2958.1554	5991.9158	0.0000	1.0000
F81	38	-3003.4772	6086.9762	0.0000	1.0000
JC69	35	-3011.6034	6096.6122	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-2867.3090	5814.6179	0.4034	0.4034
GTRG	44	-2863.9088	5815.8175	0.2215	0.6249
HKYIG	41	-2866.9848	5815.9697	0.2052	0.8301
GTRIG	45	-2863.6406	5817.2811	0.1065	0.9367
HKYI	40	-2869.5112	5819.0223	0.0446	0.9813
GTRI	44	-2866.3840	5820.7680	0.0186	0.9999
K2PG	37	-2879.4300	5832.8600	0.0000	1.0000
K2PIG	38	-2878.9629	5833.9257	0.0000	1.0000
K2PI	37	-2880.9020	5835.8040	0.0000	1.0000
SYMG	41	-2878.4045	5838.8090	0.0000	1.0000
SYMIG	42	-2877.8917	5839.7835	0.0000	1.0000
SYMI	41	-2879.5477	5841.0955	0.0000	1.0000
HKY	39	-2927.1782	5932.3563	0.0000	1.0000
GTR	43	-2924.1896	5934.3792	0.0000	1.0000
K2P	36	-2937.9620	5947.9241	0.0000	1.0000
SYM	40	-2936.2842	5952.5684	0.0000	1.0000
F81G	39	-2948.2597	5974.5195	0.0000	1.0000
F81IG	40	-2947.9641	5975.9282	0.0000	1.0000
F81I	39	-2949.9320	5977.8641	0.0000	1.0000
JC69G	36	-2956.6450	5985.2900	0.0000	1.0000
JC69IG	37	-2956.3041	5986.6083	0.0000	1.0000
JC69I	36	-2958.1554	5988.3109	0.0000	1.0000
F81	38	-3003.4772	6082.9545	0.0000	1.0000
JC69	35	-3011.6034	6093.2068	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2867.3090	6000.7840	0.7624	0.7624
K2PG	37	-2879.4300	6005.0637	0.0897	0.8521
HKYI	40	-2869.5112	6005.1884	0.0843	0.9364
HKYIG	41	-2866.9848	6006.7899	0.0378	0.9742
K2PI	37	-2880.9020	6008.0077	0.0206	0.9948
K2PIG	38	-2878.9629	6010.7835	0.0051	1.0000
GTRG	44	-2863.9088	6020.6002	0.0000	1.0000
GTRI	44	-2866.3840	6025.5507	0.0000	1.0000
GTRIG	45	-2863.6406	6026.7180	0.0000	1.0000
SYMG	41	-2878.4045	6029.6293	0.0000	1.0000
SYMI	41	-2879.5477	6031.9157	0.0000	1.0000
SYMIG	42	-2877.8917	6035.2579	0.0000	1.0000
HKY	39	-2927.1782	6113.8683	0.0000	1.0000
K2P	36	-2937.9620	6115.4736	0.0000	1.0000
GTR	43	-2924.1896	6134.5077	0.0000	1.0000
SYM	40	-2936.2842	6138.7345	0.0000	1.0000
JC69G	36	-2956.6450	6152.8395	0.0000	1.0000
JC69I	36	-2958.1554	6155.8604	0.0000	1.0000
F81G	39	-2948.2597	6156.0314	0.0000	1.0000
JC69IG	37	-2956.3041	6158.8119	0.0000	1.0000
F81I	39	-2949.9320	6159.3760	0.0000	1.0000
F81IG	40	-2947.9641	6162.0943	0.0000	1.0000
JC69	35	-3011.6034	6256.1022	0.0000	1.0000
F81	38	-3003.4772	6259.8123	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/chr1_14909.phylip = 1 - 776;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_14909.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/chr1_14909.phylip = 1 - 776;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_14909.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_14909.phylip = 1 - 776;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_14909.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

