
Output from mraic.pl version 1.4.4 by Johan Nylander
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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_5491.phylip" (19 taxa, 638 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-2089.4817	4275.9566	0.2273	0.2273
GTRG	44	-2091.0222	4276.7223	0.1550	0.3823
SYMIG	42	-2093.4438	4276.9582	0.1378	0.5201
K2PIG	38	-2098.0826	4277.1134	0.1275	0.6476
HKYIG	41	-2094.8473	4277.4731	0.1065	0.7540
SYMG	41	-2094.9701	4277.7187	0.0942	0.8482
K2PG	37	-2099.6674	4278.0214	0.0810	0.9292
HKYG	40	-2096.4350	4278.3641	0.0682	0.9974
K2PI	37	-2104.0935	4286.8737	0.0010	0.9984
HKYI	40	-2101.1359	4287.7659	0.0006	0.9990
SYMI	41	-2100.0910	4287.9606	0.0006	0.9995
GTRI	44	-2096.8547	4288.3873	0.0005	1.0000
GTR	43	-2135.6999	4363.7702	0.0000	1.0000
K2P	36	-2143.7121	4363.8569	0.0000	1.0000
SYM	40	-2139.2132	4363.9206	0.0000	1.0000
HKY	39	-2140.6249	4364.4672	0.0000	1.0000
JC69IG	37	-2162.2650	4403.2166	0.0000	1.0000
JC69G	36	-2163.5064	4403.4453	0.0000	1.0000
F81IG	40	-2159.5506	4404.5954	0.0000	1.0000
F81G	39	-2160.8091	4404.8355	0.0000	1.0000
JC69I	36	-2167.4677	4411.3680	0.0000	1.0000
F81I	39	-2164.8210	4412.8593	0.0000	1.0000
JC69	35	-2203.1794	4480.5448	0.0000	1.0000
F81	38	-2200.5808	4482.1098	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2089.4817	4268.9633	0.3440	0.3440
GTRG	44	-2091.0222	4270.0444	0.2004	0.5443
SYMIG	42	-2093.4438	4270.8877	0.1314	0.6758
HKYIG	41	-2094.8473	4271.6946	0.0878	0.7636
SYMG	41	-2094.9701	4271.9402	0.0776	0.8412
K2PIG	38	-2098.0826	4272.1651	0.0694	0.9106
HKYG	40	-2096.4350	4272.8700	0.0488	0.9594
K2PG	37	-2099.6674	4273.3347	0.0387	0.9980
GTRI	44	-2096.8547	4281.7094	0.0006	0.9986
SYMI	41	-2100.0910	4282.1821	0.0005	0.9991
K2PI	37	-2104.0935	4282.1871	0.0005	0.9996
HKYI	40	-2101.1359	4282.2717	0.0004	1.0000
GTR	43	-2135.6999	4357.3998	0.0000	1.0000
SYM	40	-2139.2132	4358.4264	0.0000	1.0000
HKY	39	-2140.6249	4359.2498	0.0000	1.0000
K2P	36	-2143.7121	4359.4243	0.0000	1.0000
JC69IG	37	-2162.2650	4398.5300	0.0000	1.0000
JC69G	36	-2163.5064	4399.0127	0.0000	1.0000
F81IG	40	-2159.5506	4399.1012	0.0000	1.0000
F81G	39	-2160.8091	4399.6181	0.0000	1.0000
JC69I	36	-2167.4677	4406.9354	0.0000	1.0000
F81I	39	-2164.8210	4407.6419	0.0000	1.0000
JC69	35	-2203.1794	4476.3588	0.0000	1.0000
F81	38	-2200.5808	4477.1615	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2099.6674	4438.2932	0.8283	0.8283
K2PIG	38	-2098.0826	4441.5820	0.1600	0.9883
K2PI	37	-2104.0935	4447.1456	0.0099	0.9982
HKYG	40	-2096.4350	4451.2035	0.0013	0.9995
HKYIG	41	-2094.8473	4454.4865	0.0003	0.9997
SYMG	41	-2094.9701	4454.7321	0.0002	0.9999
SYMIG	42	-2093.4438	4458.1379	0.0000	1.0000
HKYI	40	-2101.1359	4460.6053	0.0000	1.0000
SYMI	41	-2100.0910	4464.9739	0.0000	1.0000
GTRG	44	-2091.0222	4466.2113	0.0000	1.0000
GTRIG	45	-2089.4817	4469.5886	0.0000	1.0000
GTRI	44	-2096.8547	4477.8763	0.0000	1.0000
K2P	36	-2143.7121	4519.9245	0.0000	1.0000
HKY	39	-2140.6249	4533.1250	0.0000	1.0000
SYM	40	-2139.2132	4536.7600	0.0000	1.0000
GTR	43	-2135.6999	4549.1084	0.0000	1.0000
JC69G	36	-2163.5064	4559.5129	0.0000	1.0000
JC69IG	37	-2162.2650	4563.4885	0.0000	1.0000
JC69I	36	-2167.4677	4567.4356	0.0000	1.0000
F81G	39	-2160.8091	4573.4933	0.0000	1.0000
F81IG	40	-2159.5506	4577.4348	0.0000	1.0000
F81I	39	-2164.8210	4581.5171	0.0000	1.0000
JC69	35	-2203.1794	4632.4006	0.0000	1.0000
F81	38	-2200.5808	4646.5784	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5491.phylip = 1 - 638;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5491.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5491.phylip = 1 - 638;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5491.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr2_5491.phylip = 1 - 638;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5491.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

