
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:03 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_3279.phylip" (19 taxa, 654 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	-2678.6012	5451.7049	0.3903	0.3903
HKYG	40	-2683.5612	5452.4731	0.2658	0.6561
GTRIG	45	-2678.0205	5452.8502	0.2201	0.8762
HKYIG	41	-2683.2073	5454.0420	0.1213	0.9975
GTRI	44	-2683.9288	5462.3600	0.0019	0.9994
HKYI	40	-2689.6672	5464.6851	0.0006	1.0000
K2PG	37	-2722.9934	5524.5517	0.0000	1.0000
K2PIG	38	-2722.7391	5526.2977	0.0000	1.0000
SYMG	41	-2721.2358	5530.0990	0.0000	1.0000
SYMIG	42	-2720.9805	5531.8726	0.0000	1.0000
F81G	39	-2727.4289	5537.9392	0.0000	1.0000
F81IG	40	-2727.1834	5539.7176	0.0000	1.0000
K2PI	37	-2731.2661	5541.0971	0.0000	1.0000
SYMI	41	-2728.8442	5545.3158	0.0000	1.0000
F81I	39	-2733.9706	5551.0227	0.0000	1.0000
HKY	39	-2749.1212	5581.3239	0.0000	1.0000
GTR	43	-2745.9241	5584.0514	0.0000	1.0000
JC69G	36	-2758.8186	5593.9548	0.0000	1.0000
JC69IG	37	-2758.6024	5595.7697	0.0000	1.0000
JC69I	36	-2766.4933	5609.3043	0.0000	1.0000
K2P	36	-2787.3928	5651.1033	0.0000	1.0000
SYM	40	-2785.9786	5657.3079	0.0000	1.0000
F81	38	-2789.3558	5659.5310	0.0000	1.0000
JC69	35	-2820.7051	5715.4880	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2678.6012	5445.2024	0.4451	0.4451
GTRIG	45	-2678.0205	5446.0410	0.2926	0.7377
HKYG	40	-2683.5612	5447.1223	0.1704	0.9081
HKYIG	41	-2683.2073	5448.4145	0.0893	0.9975
GTRI	44	-2683.9288	5455.8576	0.0022	0.9996
HKYI	40	-2689.6672	5459.3343	0.0004	1.0000
K2PG	37	-2722.9934	5519.9867	0.0000	1.0000
K2PIG	38	-2722.7391	5521.4782	0.0000	1.0000
SYMG	41	-2721.2358	5524.4715	0.0000	1.0000
SYMIG	42	-2720.9805	5525.9610	0.0000	1.0000
F81G	39	-2727.4289	5532.8577	0.0000	1.0000
F81IG	40	-2727.1834	5534.3668	0.0000	1.0000
K2PI	37	-2731.2661	5536.5322	0.0000	1.0000
SYMI	41	-2728.8442	5539.6884	0.0000	1.0000
F81I	39	-2733.9706	5545.9413	0.0000	1.0000
HKY	39	-2749.1212	5576.2425	0.0000	1.0000
GTR	43	-2745.9241	5577.8481	0.0000	1.0000
JC69G	36	-2758.8186	5589.6372	0.0000	1.0000
JC69IG	37	-2758.6024	5591.2048	0.0000	1.0000
JC69I	36	-2766.4933	5604.9866	0.0000	1.0000
K2P	36	-2787.3928	5646.7856	0.0000	1.0000
SYM	40	-2785.9786	5651.9572	0.0000	1.0000
F81	38	-2789.3558	5654.7115	0.0000	1.0000
JC69	35	-2820.7051	5711.4103	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2683.5612	5626.4466	0.9449	0.9449
HKYIG	41	-2683.2073	5632.2219	0.0526	0.9976
HKYI	40	-2689.6672	5638.6586	0.0021	0.9997
GTRG	44	-2678.6012	5642.4591	0.0003	1.0000
GTRIG	45	-2678.0205	5647.7808	0.0000	1.0000
GTRI	44	-2683.9288	5653.1143	0.0000	1.0000
K2PG	37	-2722.9934	5685.8617	0.0000	1.0000
K2PIG	38	-2722.7391	5691.8362	0.0000	1.0000
K2PI	37	-2731.2661	5702.4071	0.0000	1.0000
F81G	39	-2727.4289	5707.6989	0.0000	1.0000
SYMG	41	-2721.2358	5708.2789	0.0000	1.0000
F81IG	40	-2727.1834	5713.6911	0.0000	1.0000
SYMIG	42	-2720.9805	5714.2515	0.0000	1.0000
F81I	39	-2733.9706	5720.7824	0.0000	1.0000
SYMI	41	-2728.8442	5723.4958	0.0000	1.0000
JC69G	36	-2758.8186	5751.0290	0.0000	1.0000
HKY	39	-2749.1212	5751.0837	0.0000	1.0000
JC69IG	37	-2758.6024	5757.0798	0.0000	1.0000
JC69I	36	-2766.4933	5766.3785	0.0000	1.0000
GTR	43	-2745.9241	5770.6218	0.0000	1.0000
K2P	36	-2787.3928	5808.1775	0.0000	1.0000
F81	38	-2789.3558	5825.0696	0.0000	1.0000
SYM	40	-2785.9786	5831.2815	0.0000	1.0000
JC69	35	-2820.7051	5868.3191	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_3279.phylip = 1 - 654;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_3279.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_3279.phylip = 1 - 654;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_3279.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_3279.phylip = 1 - 654;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_3279.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;


-------------------------------------------------------------
End of Output

