
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:16 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/chr1_14872.phylip" (19 taxa, 712 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: HKYIG


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	-2117.9239	4332.0641	0.9945	0.9945
GTRG	44	-2124.5184	4342.9738	0.0043	0.9988
HKYIG	41	-2129.2052	4345.5508	0.0012	1.0000
GTRI	44	-2129.8214	4353.5797	0.0000	1.0000
SYMIG	42	-2132.9564	4355.3119	0.0000	1.0000
HKYG	40	-2136.4579	4357.8041	0.0000	1.0000
K2PIG	38	-2139.4150	4359.2341	0.0000	1.0000
HKYI	40	-2138.8216	4362.5315	0.0000	1.0000
SYMG	41	-2140.7267	4368.5936	0.0000	1.0000
K2PG	37	-2147.0110	4372.1941	0.0000	1.0000
SYMI	41	-2143.5164	4374.1731	0.0000	1.0000
K2PI	37	-2149.2175	4376.6072	0.0000	1.0000
F81IG	40	-2172.6697	4430.2276	0.0000	1.0000
F81G	39	-2178.6653	4439.9735	0.0000	1.0000
F81I	39	-2180.7371	4444.1170	0.0000	1.0000
JC69IG	37	-2183.6471	4445.4662	0.0000	1.0000
JC69G	36	-2189.6141	4455.1749	0.0000	1.0000
JC69I	36	-2191.4248	4458.7963	0.0000	1.0000
GTR	43	-2205.9176	4503.4999	0.0000	1.0000
HKY	39	-2219.4466	4521.5360	0.0000	1.0000
SYM	40	-2224.2850	4533.4582	0.0000	1.0000
K2P	36	-2232.5628	4541.0723	0.0000	1.0000
F81	38	-2261.2056	4602.8154	0.0000	1.0000
JC69	35	-2273.6561	4621.0400	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2117.9239	4325.8478	0.9956	0.9956
GTRG	44	-2124.5184	4337.0368	0.0037	0.9993
HKYIG	41	-2129.2052	4340.4105	0.0007	1.0000
GTRI	44	-2129.8214	4347.6427	0.0000	1.0000
SYMIG	42	-2132.9564	4349.9128	0.0000	1.0000
HKYG	40	-2136.4579	4352.9159	0.0000	1.0000
K2PIG	38	-2139.4150	4354.8300	0.0000	1.0000
HKYI	40	-2138.8216	4357.6432	0.0000	1.0000
SYMG	41	-2140.7267	4363.4533	0.0000	1.0000
K2PG	37	-2147.0110	4368.0220	0.0000	1.0000
SYMI	41	-2143.5164	4369.0328	0.0000	1.0000
K2PI	37	-2149.2175	4372.4351	0.0000	1.0000
F81IG	40	-2172.6697	4425.3394	0.0000	1.0000
F81G	39	-2178.6653	4435.3307	0.0000	1.0000
F81I	39	-2180.7371	4439.4741	0.0000	1.0000
JC69IG	37	-2183.6471	4441.2941	0.0000	1.0000
JC69G	36	-2189.6141	4451.2282	0.0000	1.0000
JC69I	36	-2191.4248	4454.8496	0.0000	1.0000
GTR	43	-2205.9176	4497.8352	0.0000	1.0000
HKY	39	-2219.4466	4516.8931	0.0000	1.0000
SYM	40	-2224.2850	4528.5699	0.0000	1.0000
K2P	36	-2232.5628	4537.1256	0.0000	1.0000
F81	38	-2261.2056	4598.4112	0.0000	1.0000
JC69	35	-2273.6561	4617.3122	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYIG	41	-2129.2052	4527.7017	0.5281	0.5281
K2PIG	38	-2139.4150	4528.4169	0.3693	0.8974
GTRIG	45	-2117.9239	4531.4113	0.0826	0.9801
HKYG	40	-2136.4579	4535.6390	0.0100	0.9901
K2PG	37	-2147.0110	4537.0409	0.0050	0.9950
GTRG	44	-2124.5184	4538.0322	0.0030	0.9980
HKYI	40	-2138.8216	4540.3664	0.0009	0.9990
K2PI	37	-2149.2175	4541.4539	0.0005	0.9995
SYMIG	42	-2132.9564	4541.7721	0.0005	1.0000
GTRI	44	-2129.8214	4548.6381	0.0000	1.0000
SYMG	41	-2140.7267	4550.7445	0.0000	1.0000
SYMI	41	-2143.5164	4556.3240	0.0000	1.0000
F81IG	40	-2172.6697	4608.0625	0.0000	1.0000
JC69IG	37	-2183.6471	4610.3130	0.0000	1.0000
F81G	39	-2178.6653	4613.4857	0.0000	1.0000
JC69G	36	-2189.6141	4615.6790	0.0000	1.0000
F81I	39	-2180.7371	4617.6291	0.0000	1.0000
JC69I	36	-2191.4248	4619.3004	0.0000	1.0000
GTR	43	-2205.9176	4694.2625	0.0000	1.0000
HKY	39	-2219.4466	4695.0482	0.0000	1.0000
K2P	36	-2232.5628	4701.5764	0.0000	1.0000
SYM	40	-2224.2850	4711.2931	0.0000	1.0000
F81	38	-2261.2056	4771.9982	0.0000	1.0000
JC69	35	-2273.6561	4777.1949	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/chr1_14872.phylip = 1 - 712;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_14872.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/chr1_14872.phylip = 1 - 712;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_14872.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 (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_14872.phylip = 1 - 712;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_14872.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

