
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:43 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/chr20_5265.phylip" (19 taxa, 789 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	-2737.6707	5568.6641	0.6797	0.6797
GTRIG	45	-2737.4172	5570.4063	0.2845	0.9642
GTRI	44	-2741.2407	5575.8040	0.0191	0.9833
HKYG	40	-2746.2204	5576.8259	0.0115	0.9948
HKYIG	41	-2746.0178	5578.6461	0.0046	0.9994
HKYI	40	-2749.2261	5582.8372	0.0006	1.0000
SYMG	41	-2757.0493	5600.7091	0.0000	1.0000
K2PG	37	-2761.6324	5601.0091	0.0000	1.0000
SYMIG	42	-2756.8806	5602.6031	0.0000	1.0000
K2PIG	38	-2761.4167	5602.7853	0.0000	1.0000
SYMI	41	-2759.9399	5606.4903	0.0000	1.0000
K2PI	37	-2764.6528	5607.0500	0.0000	1.0000
GTR	43	-2784.6158	5660.3108	0.0000	1.0000
HKY	39	-2794.4679	5671.1013	0.0000	1.0000
F81G	39	-2803.3872	5688.9399	0.0000	1.0000
F81IG	40	-2803.2072	5690.7995	0.0000	1.0000
F81I	39	-2806.2336	5694.6327	0.0000	1.0000
SYM	40	-2805.7442	5695.8735	0.0000	1.0000
K2P	36	-2811.5557	5698.6539	0.0000	1.0000
JC69G	36	-2817.9510	5711.4445	0.0000	1.0000
JC69IG	37	-2817.7909	5713.3262	0.0000	1.0000
JC69I	36	-2820.6539	5716.8504	0.0000	1.0000
F81	38	-2850.8509	5781.6539	0.0000	1.0000
JC69	35	-2866.2224	5805.7915	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2737.6707	5563.3415	0.6587	0.6587
GTRIG	45	-2737.4172	5564.8343	0.3123	0.9710
GTRI	44	-2741.2407	5570.4814	0.0185	0.9896
HKYG	40	-2746.2204	5572.4408	0.0070	0.9965
HKYIG	41	-2746.0178	5574.0357	0.0031	0.9997
HKYI	40	-2749.2261	5578.4522	0.0003	1.0000
SYMG	41	-2757.0493	5596.0987	0.0000	1.0000
K2PG	37	-2761.6324	5597.2647	0.0000	1.0000
SYMIG	42	-2756.8806	5597.7613	0.0000	1.0000
K2PIG	38	-2761.4167	5598.8333	0.0000	1.0000
SYMI	41	-2759.9399	5601.8798	0.0000	1.0000
K2PI	37	-2764.6528	5603.3057	0.0000	1.0000
GTR	43	-2784.6158	5655.2316	0.0000	1.0000
HKY	39	-2794.4679	5666.9358	0.0000	1.0000
F81G	39	-2803.3872	5684.7744	0.0000	1.0000
F81IG	40	-2803.2072	5686.4145	0.0000	1.0000
F81I	39	-2806.2336	5690.4671	0.0000	1.0000
SYM	40	-2805.7442	5691.4885	0.0000	1.0000
K2P	36	-2811.5557	5695.1114	0.0000	1.0000
JC69G	36	-2817.9510	5707.9020	0.0000	1.0000
JC69IG	37	-2817.7909	5709.5818	0.0000	1.0000
JC69I	36	-2820.6539	5713.3078	0.0000	1.0000
F81	38	-2850.8509	5777.7019	0.0000	1.0000
JC69	35	-2866.2224	5802.4448	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2746.2204	5759.2715	0.9034	0.9034
HKYI	40	-2749.2261	5765.2829	0.0447	0.9481
HKYIG	41	-2746.0178	5765.5371	0.0394	0.9875
GTRG	44	-2737.6707	5768.8552	0.0075	0.9950
K2PG	37	-2761.6324	5770.0831	0.0041	0.9991
GTRIG	45	-2737.4172	5775.0188	0.0003	0.9994
GTRI	44	-2741.2407	5775.9952	0.0002	0.9996
K2PI	37	-2764.6528	5776.1240	0.0002	0.9998
K2PIG	38	-2761.4167	5776.3224	0.0002	1.0000
SYMG	41	-2757.0493	5787.6001	0.0000	1.0000
SYMI	41	-2759.9399	5793.3813	0.0000	1.0000
SYMIG	42	-2756.8806	5793.9334	0.0000	1.0000
HKY	39	-2794.4679	5849.0957	0.0000	1.0000
GTR	43	-2784.6158	5856.0746	0.0000	1.0000
K2P	36	-2811.5557	5863.2589	0.0000	1.0000
F81G	39	-2803.3872	5866.9343	0.0000	1.0000
F81I	39	-2806.2336	5872.6270	0.0000	1.0000
F81IG	40	-2803.2072	5873.2451	0.0000	1.0000
JC69G	36	-2817.9510	5876.0495	0.0000	1.0000
SYM	40	-2805.7442	5878.3191	0.0000	1.0000
JC69I	36	-2820.6539	5881.4554	0.0000	1.0000
JC69IG	37	-2817.7909	5882.4002	0.0000	1.0000
F81	38	-2850.8509	5955.1910	0.0000	1.0000
JC69	35	-2866.2224	5965.9217	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/chr20_5265.phylip = 1 - 789;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr20_5265.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/chr20_5265.phylip = 1 - 789;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr20_5265.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/chr20_5265.phylip = 1 - 789;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr20_5265.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

