
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:45 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_22625.phylip" (19 taxa, 487 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	-2083.7353	4264.4300	0.4129	0.4129
HKYG	40	-2088.8608	4265.0759	0.2989	0.7118
GTRIG	45	-2083.4125	4266.2127	0.1693	0.8811
HKYIG	41	-2088.6145	4266.9683	0.1160	0.9972
GTRI	44	-2089.2250	4275.4093	0.0017	0.9989
HKYI	40	-2094.4279	4276.2101	0.0011	1.0000
K2PG	37	-2113.7921	4307.8471	0.0000	1.0000
K2PIG	38	-2113.5721	4309.7602	0.0000	1.0000
SYMG	41	-2112.5861	4314.9115	0.0000	1.0000
SYMIG	42	-2112.3542	4316.8436	0.0000	1.0000
K2PI	37	-2119.4084	4319.0796	0.0000	1.0000
SYMI	41	-2118.1337	4326.0066	0.0000	1.0000
F81G	39	-2132.3010	4349.5818	0.0000	1.0000
F81IG	40	-2132.1564	4351.6671	0.0000	1.0000
F81I	39	-2137.0198	4359.0194	0.0000	1.0000
JC69G	36	-2150.3068	4378.5335	0.0000	1.0000
JC69IG	37	-2150.1686	4380.6000	0.0000	1.0000
JC69I	36	-2154.8977	4387.7154	0.0000	1.0000
GTR	43	-2154.5871	4403.7161	0.0000	1.0000
HKY	39	-2160.2786	4405.5370	0.0000	1.0000
K2P	36	-2183.1599	4444.2398	0.0000	1.0000
SYM	40	-2180.3089	4447.9720	0.0000	1.0000
F81	38	-2198.8712	4480.3585	0.0000	1.0000
JC69	35	-2216.0649	4507.7174	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2083.7353	4255.4707	0.5024	0.5024
GTRIG	45	-2083.4125	4256.8250	0.2552	0.7576
HKYG	40	-2088.8608	4257.7217	0.1630	0.9206
HKYIG	41	-2088.6145	4259.2290	0.0767	0.9973
GTRI	44	-2089.2250	4266.4500	0.0021	0.9994
HKYI	40	-2094.4279	4268.8559	0.0006	1.0000
K2PG	37	-2113.7921	4301.5843	0.0000	1.0000
K2PIG	38	-2113.5721	4303.1441	0.0000	1.0000
SYMG	41	-2112.5861	4307.1721	0.0000	1.0000
SYMIG	42	-2112.3542	4308.7084	0.0000	1.0000
K2PI	37	-2119.4084	4312.8168	0.0000	1.0000
SYMI	41	-2118.1337	4318.2673	0.0000	1.0000
F81G	39	-2132.3010	4342.6019	0.0000	1.0000
F81IG	40	-2132.1564	4344.3128	0.0000	1.0000
F81I	39	-2137.0198	4352.0396	0.0000	1.0000
JC69G	36	-2150.3068	4372.6135	0.0000	1.0000
JC69IG	37	-2150.1686	4374.3372	0.0000	1.0000
JC69I	36	-2154.8977	4381.7954	0.0000	1.0000
GTR	43	-2154.5871	4395.1743	0.0000	1.0000
HKY	39	-2160.2786	4398.5571	0.0000	1.0000
K2P	36	-2183.1599	4438.3198	0.0000	1.0000
SYM	40	-2180.3089	4440.6178	0.0000	1.0000
F81	38	-2198.8712	4473.7425	0.0000	1.0000
JC69	35	-2216.0649	4502.1298	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2088.8608	4425.2522	0.9411	0.9411
HKYIG	41	-2088.6145	4430.9478	0.0546	0.9957
HKYI	40	-2094.4279	4436.3864	0.0036	0.9993
GTRG	44	-2083.7353	4439.7543	0.0007	1.0000
GTRIG	45	-2083.4125	4445.2969	0.0000	1.0000
GTRI	44	-2089.2250	4450.7336	0.0000	1.0000
K2PG	37	-2113.7921	4456.5500	0.0000	1.0000
K2PIG	38	-2113.5721	4462.2981	0.0000	1.0000
K2PI	37	-2119.4084	4467.7826	0.0000	1.0000
SYMG	41	-2112.5861	4478.8910	0.0000	1.0000
SYMIG	42	-2112.3542	4484.6155	0.0000	1.0000
SYMI	41	-2118.1337	4489.9861	0.0000	1.0000
F81G	39	-2132.3010	4505.9442	0.0000	1.0000
F81IG	40	-2132.1564	4511.8434	0.0000	1.0000
F81I	39	-2137.0198	4515.3819	0.0000	1.0000
JC69G	36	-2150.3068	4523.3910	0.0000	1.0000
JC69IG	37	-2150.1686	4529.3030	0.0000	1.0000
JC69I	36	-2154.8977	4532.5729	0.0000	1.0000
HKY	39	-2160.2786	4561.8994	0.0000	1.0000
GTR	43	-2154.5871	4575.2697	0.0000	1.0000
K2P	36	-2183.1599	4589.0973	0.0000	1.0000
SYM	40	-2180.3089	4608.1483	0.0000	1.0000
F81	38	-2198.8712	4632.8965	0.0000	1.0000
JC69	35	-2216.0649	4648.7190	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_22625.phylip = 1 - 487;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22625.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_22625.phylip = 1 - 487;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22625.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_22625.phylip = 1 - 487;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22625.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

