
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:02 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/chr10_4411.phylip" (19 taxa, 577 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-2131.7823	4359.0082	0.5894	0.5894
GTRIG	45	-2131.4992	4360.7949	0.2412	0.8306
HKYG	40	-2138.2190	4362.5573	0.0999	0.9306
GTRI	44	-2134.8665	4365.1765	0.0270	0.9575
HKYIG	41	-2138.4678	4365.3731	0.0245	0.9820
HKYI	40	-2140.3720	4366.8634	0.0116	0.9936
K2PG	37	-2145.0452	4369.3074	0.0034	0.9970
K2PIG	38	-2145.0184	4371.5461	0.0011	0.9981
K2PI	37	-2146.2475	4371.7121	0.0010	0.9991
SYMG	41	-2142.2414	4372.9202	0.0006	0.9997
SYMIG	42	-2142.1934	4375.1508	0.0002	0.9999
SYMI	41	-2143.9143	4376.2659	0.0001	1.0000
GTR	43	-2177.1933	4447.4861	0.0000	1.0000
HKY	39	-2183.2698	4450.3496	0.0000	1.0000
K2P	36	-2191.1669	4459.2671	0.0000	1.0000
SYM	40	-2186.6920	4459.5034	0.0000	1.0000
F81G	39	-2201.9092	4487.6284	0.0000	1.0000
F81IG	40	-2201.8145	4489.7485	0.0000	1.0000
F81I	39	-2203.0530	4489.9160	0.0000	1.0000
JC69G	36	-2206.9009	4490.7351	0.0000	1.0000
JC69I	36	-2207.8319	4492.5972	0.0000	1.0000
JC69IG	37	-2206.8012	4492.8194	0.0000	1.0000
F81	38	-2242.9269	4567.3631	0.0000	1.0000
JC69	35	-2248.2008	4571.0597	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2131.7823	4351.5646	0.6021	0.6021
GTRIG	45	-2131.4992	4352.9983	0.2940	0.8961
HKYG	40	-2138.2190	4356.4379	0.0527	0.9488
GTRI	44	-2134.8665	4357.7329	0.0276	0.9763
HKYIG	41	-2138.4678	4358.9357	0.0151	0.9914
HKYI	40	-2140.3720	4360.7440	0.0061	0.9975
K2PG	37	-2145.0452	4364.0904	0.0011	0.9987
K2PIG	38	-2145.0184	4366.0368	0.0004	0.9991
SYMG	41	-2142.2414	4366.4828	0.0003	0.9995
K2PI	37	-2146.2475	4366.4950	0.0003	0.9998
SYMIG	42	-2142.1934	4368.3867	0.0001	0.9999
SYMI	41	-2143.9143	4369.8285	0.0001	1.0000
GTR	43	-2177.1933	4440.3867	0.0000	1.0000
HKY	39	-2183.2698	4444.5395	0.0000	1.0000
SYM	40	-2186.6920	4453.3840	0.0000	1.0000
K2P	36	-2191.1669	4454.3338	0.0000	1.0000
F81G	39	-2201.9092	4481.8184	0.0000	1.0000
F81IG	40	-2201.8145	4483.6291	0.0000	1.0000
F81I	39	-2203.0530	4484.1060	0.0000	1.0000
JC69G	36	-2206.9009	4485.8017	0.0000	1.0000
JC69IG	37	-2206.8012	4487.6023	0.0000	1.0000
JC69I	36	-2207.8319	4487.6638	0.0000	1.0000
F81	38	-2242.9269	4561.8538	0.0000	1.0000
JC69	35	-2248.2008	4566.4017	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2145.0452	4525.3305	0.7043	0.7043
K2PI	37	-2146.2475	4527.7352	0.2116	0.9159
HKYG	40	-2138.2190	4530.7516	0.0468	0.9628
K2PIG	38	-2145.0184	4531.6348	0.0301	0.9929
HKYI	40	-2140.3720	4535.0577	0.0054	0.9983
HKYIG	41	-2138.4678	4537.6072	0.0015	0.9999
GTRG	44	-2131.7823	4543.3097	0.0001	0.9999
SYMG	41	-2142.2414	4545.1544	0.0000	1.0000
SYMI	41	-2143.9143	4548.5001	0.0000	1.0000
GTRIG	45	-2131.4992	4549.1012	0.0000	1.0000
GTRI	44	-2134.8665	4549.4780	0.0000	1.0000
SYMIG	42	-2142.1934	4551.4161	0.0000	1.0000
K2P	36	-2191.1669	4611.2161	0.0000	1.0000
HKY	39	-2183.2698	4614.4954	0.0000	1.0000
SYM	40	-2186.6920	4627.6977	0.0000	1.0000
GTR	43	-2177.1933	4627.7739	0.0000	1.0000
JC69G	36	-2206.9009	4642.6840	0.0000	1.0000
JC69I	36	-2207.8319	4644.5462	0.0000	1.0000
JC69IG	37	-2206.8012	4648.8425	0.0000	1.0000
F81G	39	-2201.9092	4651.7742	0.0000	1.0000
F81I	39	-2203.0530	4654.0618	0.0000	1.0000
F81IG	40	-2201.8145	4657.9428	0.0000	1.0000
JC69	35	-2248.2008	4718.9262	0.0000	1.0000
F81	38	-2242.9269	4727.4518	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/chr10_4411.phylip = 1 - 577;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4411.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/chr10_4411.phylip = 1 - 577;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4411.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4411.phylip = 1 - 577;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4411.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

