
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:05 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/chr2_21402.phylip" (19 taxa, 589 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	-2165.5323	4426.3441	0.7261	0.7261
GTRIG	45	-2165.3545	4428.3334	0.2686	0.9947
GTRI	44	-2170.5906	4436.4607	0.0046	0.9993
HKYG	40	-2177.4270	4440.8394	0.0005	0.9998
HKYIG	41	-2177.2430	4442.7822	0.0002	1.0000
HKYI	40	-2181.9608	4449.9071	0.0000	1.0000
SYMG	41	-2192.3160	4472.9282	0.0000	1.0000
SYMIG	42	-2192.0520	4474.7193	0.0000	1.0000
K2PG	37	-2198.5991	4476.3016	0.0000	1.0000
K2PIG	38	-2198.3404	4478.0699	0.0000	1.0000
SYMI	41	-2197.5948	4483.4859	0.0000	1.0000
GTR	43	-2195.7295	4484.4021	0.0000	1.0000
K2PI	37	-2203.9614	4487.0262	0.0000	1.0000
HKY	39	-2205.7755	4495.2340	0.0000	1.0000
SYM	40	-2222.1414	4530.2682	0.0000	1.0000
K2P	36	-2227.7798	4532.3856	0.0000	1.0000
F81G	39	-2240.2285	4564.1402	0.0000	1.0000
F81IG	40	-2240.0825	4566.1503	0.0000	1.0000
F81I	39	-2244.1490	4571.9811	0.0000	1.0000
JC69G	36	-2256.1656	4589.1573	0.0000	1.0000
JC69IG	37	-2255.9937	4591.0908	0.0000	1.0000
JC69I	36	-2259.9766	4596.7793	0.0000	1.0000
F81	38	-2266.3693	4614.1278	0.0000	1.0000
JC69	35	-2282.9009	4640.3587	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2165.5323	4419.0647	0.6914	0.6914
GTRIG	45	-2165.3545	4420.7091	0.3038	0.9952
GTRI	44	-2170.5906	4429.1813	0.0044	0.9996
HKYG	40	-2177.4270	4434.8540	0.0003	0.9999
HKYIG	41	-2177.2430	4436.4860	0.0001	1.0000
HKYI	40	-2181.9608	4443.9217	0.0000	1.0000
SYMG	41	-2192.3160	4466.6320	0.0000	1.0000
SYMIG	42	-2192.0520	4468.1039	0.0000	1.0000
K2PG	37	-2198.5991	4471.1982	0.0000	1.0000
K2PIG	38	-2198.3404	4472.6808	0.0000	1.0000
SYMI	41	-2197.5948	4477.1897	0.0000	1.0000
GTR	43	-2195.7295	4477.4590	0.0000	1.0000
K2PI	37	-2203.9614	4481.9227	0.0000	1.0000
HKY	39	-2205.7755	4489.5510	0.0000	1.0000
SYM	40	-2222.1414	4524.2828	0.0000	1.0000
K2P	36	-2227.7798	4527.5596	0.0000	1.0000
F81G	39	-2240.2285	4558.4571	0.0000	1.0000
F81IG	40	-2240.0825	4560.1649	0.0000	1.0000
F81I	39	-2244.1490	4566.2980	0.0000	1.0000
JC69G	36	-2256.1656	4584.3313	0.0000	1.0000
JC69IG	37	-2255.9937	4585.9874	0.0000	1.0000
JC69I	36	-2259.9766	4591.9532	0.0000	1.0000
F81	38	-2266.3693	4608.7387	0.0000	1.0000
JC69	35	-2282.9009	4635.8018	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2177.4270	4609.9911	0.6640	0.6640
GTRG	44	-2165.5323	4611.7154	0.2804	0.9444
HKYIG	41	-2177.2430	4616.0015	0.0329	0.9773
GTRIG	45	-2165.3545	4617.7382	0.0138	0.9911
HKYI	40	-2181.9608	4619.0587	0.0071	0.9982
GTRI	44	-2170.5906	4621.8320	0.0018	1.0000
K2PG	37	-2198.5991	4633.1999	0.0000	1.0000
K2PIG	38	-2198.3404	4639.0610	0.0000	1.0000
K2PI	37	-2203.9614	4643.9245	0.0000	1.0000
SYMG	41	-2192.3160	4646.1475	0.0000	1.0000
SYMIG	42	-2192.0520	4651.9978	0.0000	1.0000
SYMI	41	-2197.5948	4656.7052	0.0000	1.0000
HKY	39	-2205.7755	4660.3096	0.0000	1.0000
GTR	43	-2195.7295	4665.7313	0.0000	1.0000
K2P	36	-2227.7798	4685.1829	0.0000	1.0000
SYM	40	-2222.1414	4699.4199	0.0000	1.0000
F81G	39	-2240.2285	4729.2157	0.0000	1.0000
F81IG	40	-2240.0825	4735.3020	0.0000	1.0000
F81I	39	-2244.1490	4737.0566	0.0000	1.0000
JC69G	36	-2256.1656	4741.9546	0.0000	1.0000
JC69IG	37	-2255.9937	4747.9891	0.0000	1.0000
JC69I	36	-2259.9766	4749.5766	0.0000	1.0000
F81	38	-2266.3693	4775.1189	0.0000	1.0000
JC69	35	-2282.9009	4789.0467	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/chr2_21402.phylip = 1 - 589;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21402.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/chr2_21402.phylip = 1 - 589;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21402.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/chr2_21402.phylip = 1 - 589;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21402.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

