
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:06 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/chrZ_14680.phylip" (19 taxa, 952 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	-2301.0488	4694.4636	0.2979	0.2979
GTRI	44	-2301.4297	4695.2255	0.2035	0.5015
HKYG	40	-2305.9198	4695.4401	0.1828	0.6843
HKYI	40	-2306.3071	4696.2147	0.1241	0.8084
GTRIG	45	-2300.8722	4696.3140	0.1181	0.9265
HKYIG	41	-2305.7397	4697.2641	0.0734	1.0000
SYMG	41	-2315.5817	4716.9481	0.0000	1.0000
SYMI	41	-2316.1320	4718.0485	0.0000	1.0000
K2PG	37	-2320.5524	4718.1814	0.0000	1.0000
SYMIG	42	-2315.3535	4718.6807	0.0000	1.0000
K2PI	37	-2321.0323	4719.1413	0.0000	1.0000
K2PIG	38	-2320.3490	4719.9444	0.0000	1.0000
GTR	43	-2317.8691	4725.9056	0.0000	1.0000
HKY	39	-2322.8476	4727.1163	0.0000	1.0000
SYM	40	-2331.4016	4746.4037	0.0000	1.0000
K2P	36	-2336.7348	4748.3811	0.0000	1.0000
F81G	39	-2334.1567	4749.7344	0.0000	1.0000
F81I	39	-2334.5239	4750.4689	0.0000	1.0000
F81IG	40	-2334.0192	4751.6389	0.0000	1.0000
JC69G	36	-2347.3554	4769.6224	0.0000	1.0000
JC69I	36	-2347.7679	4770.4472	0.0000	1.0000
JC69IG	37	-2347.2111	4771.4988	0.0000	1.0000
F81	38	-2349.9951	4779.2366	0.0000	1.0000
JC69	35	-2362.8837	4798.5185	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2301.0488	4690.0975	0.3323	0.3323
GTRI	44	-2301.4297	4690.8594	0.2270	0.5594
GTRIG	45	-2300.8722	4691.7444	0.1459	0.7052
HKYG	40	-2305.9198	4691.8396	0.1391	0.8443
HKYI	40	-2306.3071	4692.6143	0.0944	0.9387
HKYIG	41	-2305.7397	4693.4794	0.0613	1.0000
SYMG	41	-2315.5817	4713.1634	0.0000	1.0000
SYMI	41	-2316.1320	4714.2639	0.0000	1.0000
SYMIG	42	-2315.3535	4714.7071	0.0000	1.0000
K2PG	37	-2320.5524	4715.1048	0.0000	1.0000
K2PI	37	-2321.0323	4716.0647	0.0000	1.0000
K2PIG	38	-2320.3490	4716.6980	0.0000	1.0000
GTR	43	-2317.8691	4721.7382	0.0000	1.0000
HKY	39	-2322.8476	4723.6953	0.0000	1.0000
SYM	40	-2331.4016	4742.8032	0.0000	1.0000
K2P	36	-2336.7348	4745.4696	0.0000	1.0000
F81G	39	-2334.1567	4746.3133	0.0000	1.0000
F81I	39	-2334.5239	4747.0478	0.0000	1.0000
F81IG	40	-2334.0192	4748.0384	0.0000	1.0000
JC69G	36	-2347.3554	4766.7109	0.0000	1.0000
JC69I	36	-2347.7679	4767.5357	0.0000	1.0000
JC69IG	37	-2347.2111	4768.4222	0.0000	1.0000
F81	38	-2349.9951	4775.9902	0.0000	1.0000
JC69	35	-2362.8837	4795.7674	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2305.9198	4886.1822	0.5749	0.5749
HKYI	40	-2306.3071	4886.9569	0.3903	0.9652
HKYIG	41	-2305.7397	4892.6806	0.0223	0.9875
K2PG	37	-2320.5524	4894.8717	0.0075	0.9949
K2PI	37	-2321.0323	4895.8316	0.0046	0.9996
K2PIG	38	-2320.3490	4901.3235	0.0003	0.9999
GTRG	44	-2301.0488	4903.8744	0.0001	0.9999
GTRI	44	-2301.4297	4904.6363	0.0001	1.0000
GTRIG	45	-2300.8722	4910.3799	0.0000	1.0000
SYMG	41	-2315.5817	4912.3646	0.0000	1.0000
HKY	39	-2322.8476	4913.1793	0.0000	1.0000
SYMI	41	-2316.1320	4913.4651	0.0000	1.0000
SYMIG	42	-2315.3535	4918.7668	0.0000	1.0000
K2P	36	-2336.7348	4920.3779	0.0000	1.0000
GTR	43	-2317.8691	4930.6565	0.0000	1.0000
F81G	39	-2334.1567	4935.7974	0.0000	1.0000
F81I	39	-2334.5239	4936.5318	0.0000	1.0000
SYM	40	-2331.4016	4937.1458	0.0000	1.0000
JC69G	36	-2347.3554	4941.6192	0.0000	1.0000
F81IG	40	-2334.0192	4942.3810	0.0000	1.0000
JC69I	36	-2347.7679	4942.4441	0.0000	1.0000
JC69IG	37	-2347.2111	4948.1891	0.0000	1.0000
F81	38	-2349.9951	4960.6156	0.0000	1.0000
JC69	35	-2362.8837	4965.8172	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/chrZ_14680.phylip = 1 - 952;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_14680.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/chrZ_14680.phylip = 1 - 952;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_14680.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/chrZ_14680.phylip = 1 - 952;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_14680.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

