
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:06 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_5056.phylip" (19 taxa, 559 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	-2667.9942	5431.6928	0.7248	0.7248
GTRIG	45	-2667.9940	5434.0581	0.2221	0.9469
HKYG	40	-2675.5661	5437.4642	0.0405	0.9874
HKYIG	41	-2675.5660	5439.7935	0.0126	1.0000
GTRI	44	-2679.4819	5454.6680	0.0000	1.0000
HKYI	40	-2684.7857	5455.9034	0.0000	1.0000
K2PG	37	-2688.3217	5456.0408	0.0000	1.0000
K2PIG	38	-2688.3215	5458.3430	0.0000	1.0000
SYMG	41	-2685.3128	5459.2870	0.0000	1.0000
SYMIG	42	-2685.3126	5461.6252	0.0000	1.0000
K2PI	37	-2696.2428	5471.8830	0.0000	1.0000
SYMI	41	-2693.2970	5475.2556	0.0000	1.0000
GTR	43	-2736.3707	5566.0890	0.0000	1.0000
HKY	39	-2745.6453	5575.3022	0.0000	1.0000
K2P	36	-2761.4075	5599.9183	0.0000	1.0000
SYM	40	-2757.3332	5600.9985	0.0000	1.0000
F81G	39	-2776.4584	5636.9284	0.0000	1.0000
F81IG	40	-2776.4585	5639.2490	0.0000	1.0000
F81I	39	-2783.2736	5650.5587	0.0000	1.0000
JC69G	36	-2787.3036	5651.7107	0.0000	1.0000
JC69IG	37	-2787.3036	5654.0045	0.0000	1.0000
JC69I	36	-2793.4285	5663.9604	0.0000	1.0000
F81	38	-2850.2836	5782.2672	0.0000	1.0000
JC69	35	-2862.7947	5800.4078	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2667.9942	5423.9885	0.7110	0.7110
GTRIG	45	-2667.9940	5425.9880	0.2616	0.9727
HKYG	40	-2675.5661	5431.1322	0.0200	0.9926
HKYIG	41	-2675.5660	5433.1320	0.0074	1.0000
GTRI	44	-2679.4819	5446.9637	0.0000	1.0000
HKYI	40	-2684.7857	5449.5714	0.0000	1.0000
K2PG	37	-2688.3217	5450.6435	0.0000	1.0000
SYMG	41	-2685.3128	5452.6255	0.0000	1.0000
K2PIG	38	-2688.3215	5452.6430	0.0000	1.0000
SYMIG	42	-2685.3126	5454.6252	0.0000	1.0000
K2PI	37	-2696.2428	5466.4857	0.0000	1.0000
SYMI	41	-2693.2970	5468.5941	0.0000	1.0000
GTR	43	-2736.3707	5558.7414	0.0000	1.0000
HKY	39	-2745.6453	5569.2906	0.0000	1.0000
SYM	40	-2757.3332	5594.6665	0.0000	1.0000
K2P	36	-2761.4075	5594.8149	0.0000	1.0000
F81G	39	-2776.4584	5630.9169	0.0000	1.0000
F81IG	40	-2776.4585	5632.9169	0.0000	1.0000
F81I	39	-2783.2736	5644.5472	0.0000	1.0000
JC69G	36	-2787.3036	5646.6073	0.0000	1.0000
JC69IG	37	-2787.3036	5648.6071	0.0000	1.0000
JC69I	36	-2793.4285	5658.8570	0.0000	1.0000
F81	38	-2850.2836	5776.5672	0.0000	1.0000
JC69	35	-2862.7947	5795.5894	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2675.5661	5604.1782	0.9186	0.9186
HKYIG	41	-2675.5660	5610.5041	0.0389	0.9574
K2PG	37	-2688.3217	5610.7110	0.0350	0.9925
GTRG	44	-2667.9942	5614.3391	0.0057	0.9982
K2PIG	38	-2688.3215	5617.0367	0.0015	0.9997
GTRIG	45	-2667.9940	5620.6647	0.0002	0.9999
HKYI	40	-2684.7857	5622.6174	0.0001	1.0000
K2PI	37	-2696.2428	5626.5532	0.0000	1.0000
SYMG	41	-2685.3128	5629.9976	0.0000	1.0000
SYMIG	42	-2685.3126	5636.3234	0.0000	1.0000
GTRI	44	-2679.4819	5637.3143	0.0000	1.0000
SYMI	41	-2693.2970	5645.9662	0.0000	1.0000
HKY	39	-2745.6453	5738.0105	0.0000	1.0000
GTR	43	-2736.3707	5744.7658	0.0000	1.0000
K2P	36	-2761.4075	5750.5563	0.0000	1.0000
SYM	40	-2757.3332	5767.7124	0.0000	1.0000
F81G	39	-2776.4584	5799.6367	0.0000	1.0000
JC69G	36	-2787.3036	5802.3486	0.0000	1.0000
F81IG	40	-2776.4585	5805.9629	0.0000	1.0000
JC69IG	37	-2787.3036	5808.6747	0.0000	1.0000
F81I	39	-2783.2736	5813.2670	0.0000	1.0000
JC69I	36	-2793.4285	5814.5984	0.0000	1.0000
F81	38	-2850.2836	5940.9609	0.0000	1.0000
JC69	35	-2862.7947	5947.0047	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_5056.phylip = 1 - 559;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_5056.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_5056.phylip = 1 - 559;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_5056.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_5056.phylip = 1 - 559;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_5056.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

