
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:34 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/chr5_2303.phylip" (19 taxa, 683 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-2077.4531	4251.4053	0.4547	0.4547
GTRG	44	-2078.8567	4251.9203	0.3515	0.8061
HKYIG	41	-2083.1737	4253.7203	0.1429	0.9490
HKYG	40	-2085.4277	4255.9645	0.0465	0.9956
GTRI	44	-2083.3362	4260.8793	0.0040	0.9996
HKYI	40	-2090.0724	4265.2539	0.0004	1.0000
F81G	39	-2109.2682	4301.3886	0.0000	1.0000
F81IG	40	-2108.2108	4301.5307	0.0000	1.0000
F81I	39	-2114.3578	4311.5679	0.0000	1.0000
SYMIG	42	-2115.1276	4319.8989	0.0000	1.0000
SYMG	41	-2116.5217	4320.4163	0.0000	1.0000
K2PIG	38	-2124.7918	4330.1862	0.0000	1.0000
K2PG	37	-2125.9497	4330.2591	0.0000	1.0000
SYMI	41	-2121.4829	4330.3387	0.0000	1.0000
K2PI	37	-2129.1566	4336.6730	0.0000	1.0000
GTR	43	-2123.1615	4338.2447	0.0000	1.0000
HKY	39	-2129.0979	4341.0481	0.0000	1.0000
F81	38	-2150.2413	4381.0850	0.0000	1.0000
JC69G	36	-2154.3906	4384.9051	0.0000	1.0000
JC69IG	37	-2153.3505	4385.0607	0.0000	1.0000
JC69I	36	-2157.6679	4391.4597	0.0000	1.0000
SYM	40	-2158.9954	4403.0999	0.0000	1.0000
K2P	36	-2167.1712	4410.4662	0.0000	1.0000
JC69	35	-2193.1176	4460.1301	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2077.4531	4244.9061	0.5247	0.5247
GTRG	44	-2078.8567	4245.7134	0.3504	0.8751
HKYIG	41	-2083.1737	4248.3474	0.0939	0.9690
HKYG	40	-2085.4277	4250.8554	0.0268	0.9958
GTRI	44	-2083.3362	4254.6724	0.0040	0.9997
HKYI	40	-2090.0724	4260.1449	0.0003	1.0000
F81IG	40	-2108.2108	4296.4217	0.0000	1.0000
F81G	39	-2109.2682	4296.5363	0.0000	1.0000
F81I	39	-2114.3578	4306.7156	0.0000	1.0000
SYMIG	42	-2115.1276	4314.2551	0.0000	1.0000
SYMG	41	-2116.5217	4315.0435	0.0000	1.0000
SYMI	41	-2121.4829	4324.9659	0.0000	1.0000
K2PIG	38	-2124.7918	4325.5837	0.0000	1.0000
K2PG	37	-2125.9497	4325.8995	0.0000	1.0000
K2PI	37	-2129.1566	4332.3133	0.0000	1.0000
GTR	43	-2123.1615	4332.3230	0.0000	1.0000
HKY	39	-2129.0979	4336.1959	0.0000	1.0000
F81	38	-2150.2413	4376.4825	0.0000	1.0000
JC69IG	37	-2153.3505	4380.7010	0.0000	1.0000
JC69G	36	-2154.3906	4380.7812	0.0000	1.0000
JC69I	36	-2157.6679	4387.3358	0.0000	1.0000
SYM	40	-2158.9954	4397.9908	0.0000	1.0000
K2P	36	-2167.1712	4406.3423	0.0000	1.0000
JC69	35	-2193.1176	4456.2352	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2085.4277	4431.9152	0.7268	0.7268
HKYIG	41	-2083.1737	4433.9337	0.2649	0.9917
HKYI	40	-2090.0724	4441.2047	0.0070	0.9987
GTRG	44	-2078.8567	4444.8792	0.0011	0.9998
GTRIG	45	-2077.4531	4448.5984	0.0002	1.0000
GTRI	44	-2083.3362	4453.8382	0.0000	1.0000
F81G	39	-2109.2682	4473.0696	0.0000	1.0000
F81IG	40	-2108.2108	4477.4815	0.0000	1.0000
F81I	39	-2114.3578	4483.2489	0.0000	1.0000
K2PG	37	-2125.9497	4493.3798	0.0000	1.0000
K2PIG	38	-2124.7918	4497.5905	0.0000	1.0000
K2PI	37	-2129.1566	4499.7936	0.0000	1.0000
SYMG	41	-2116.5217	4500.6298	0.0000	1.0000
SYMIG	42	-2115.1276	4504.3679	0.0000	1.0000
SYMI	41	-2121.4829	4510.5522	0.0000	1.0000
HKY	39	-2129.0979	4512.7292	0.0000	1.0000
GTR	43	-2123.1615	4526.9622	0.0000	1.0000
JC69G	36	-2154.3906	4543.7350	0.0000	1.0000
JC69IG	37	-2153.3505	4548.1813	0.0000	1.0000
F81	38	-2150.2413	4548.4893	0.0000	1.0000
JC69I	36	-2157.6679	4550.2897	0.0000	1.0000
K2P	36	-2167.1712	4569.2961	0.0000	1.0000
SYM	40	-2158.9954	4579.0506	0.0000	1.0000
JC69	35	-2193.1176	4614.6625	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/chr5_2303.phylip = 1 - 683;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2303.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/chr5_2303.phylip = 1 - 683;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2303.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2303.phylip = 1 - 683;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2303.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

