
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:01 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/chr11_3426.phylip" (19 taxa, 626 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
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
HKYG	40	-2307.1506	4699.9081	0.4078	0.4078
GTRG	44	-2302.8437	4700.5032	0.3029	0.7107
HKYIG	41	-2307.1507	4702.1987	0.1297	0.8404
GTRIG	45	-2302.8439	4702.8257	0.0948	0.9352
HKYI	40	-2309.2944	4704.1956	0.0478	0.9830
GTRI	44	-2305.7523	4706.3203	0.0165	0.9996
HKY	39	-2315.6910	4714.7063	0.0002	0.9998
GTR	43	-2311.4342	4715.3700	0.0002	1.0000
K2PG	37	-2321.4471	4721.6766	0.0000	1.0000
K2PIG	38	-2321.4472	4723.9438	0.0000	1.0000
K2PI	37	-2323.1947	4725.1718	0.0000	1.0000
SYMG	41	-2320.3358	4728.5689	0.0000	1.0000
SYMIG	42	-2320.3358	4730.8672	0.0000	1.0000
SYMI	41	-2322.3159	4732.5291	0.0000	1.0000
K2P	36	-2329.9125	4736.3480	0.0000	1.0000
SYM	40	-2328.8249	4743.2567	0.0000	1.0000
F81G	39	-2351.8607	4787.0456	0.0000	1.0000
F81IG	40	-2351.8607	4789.3283	0.0000	1.0000
F81I	39	-2353.3092	4789.9427	0.0000	1.0000
F81	38	-2358.7407	4798.5308	0.0000	1.0000
JC69G	36	-2365.5995	4807.7218	0.0000	1.0000
JC69IG	37	-2365.5995	4809.9812	0.0000	1.0000
JC69I	36	-2366.9839	4810.4907	0.0000	1.0000
JC69	35	-2372.6029	4819.4770	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2302.8437	4693.6873	0.3975	0.3975
HKYG	40	-2307.1506	4694.3013	0.2924	0.6899
GTRIG	45	-2302.8439	4695.6878	0.1462	0.8361
HKYIG	41	-2307.1507	4696.3014	0.1076	0.9437
HKYI	40	-2309.2944	4698.5887	0.0343	0.9780
GTRI	44	-2305.7523	4699.5045	0.0217	0.9996
GTR	43	-2311.4342	4708.8683	0.0002	0.9998
HKY	39	-2315.6910	4709.3821	0.0002	1.0000
K2PG	37	-2321.4471	4716.8943	0.0000	1.0000
K2PIG	38	-2321.4472	4718.8944	0.0000	1.0000
K2PI	37	-2323.1947	4720.3895	0.0000	1.0000
SYMG	41	-2320.3358	4722.6716	0.0000	1.0000
SYMIG	42	-2320.3358	4724.6717	0.0000	1.0000
SYMI	41	-2322.3159	4726.6318	0.0000	1.0000
K2P	36	-2329.9125	4731.8251	0.0000	1.0000
SYM	40	-2328.8249	4737.6498	0.0000	1.0000
F81G	39	-2351.8607	4781.7213	0.0000	1.0000
F81IG	40	-2351.8607	4783.7215	0.0000	1.0000
F81I	39	-2353.3092	4784.6184	0.0000	1.0000
F81	38	-2358.7407	4793.4814	0.0000	1.0000
JC69G	36	-2365.5995	4803.1989	0.0000	1.0000
JC69IG	37	-2365.5995	4805.1989	0.0000	1.0000
JC69I	36	-2366.9839	4805.9677	0.0000	1.0000
JC69	35	-2372.6029	4815.2058	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2307.1506	4871.8753	0.8517	0.8517
HKYI	40	-2309.2944	4876.1627	0.0998	0.9516
HKYIG	41	-2307.1507	4878.3148	0.0340	0.9856
K2PG	37	-2321.4471	4881.1502	0.0082	0.9938
HKY	39	-2315.6910	4882.5168	0.0042	0.9980
K2PI	37	-2323.1947	4884.6454	0.0014	0.9994
K2PIG	38	-2321.4472	4887.5897	0.0003	0.9998
GTRG	44	-2302.8437	4889.0188	0.0002	0.9999
K2P	36	-2329.9125	4891.6417	0.0000	1.0000
GTRI	44	-2305.7523	4894.8359	0.0000	1.0000
GTRIG	45	-2302.8439	4895.4585	0.0000	1.0000
GTR	43	-2311.4342	4899.7604	0.0000	1.0000
SYMG	41	-2320.3358	4904.6850	0.0000	1.0000
SYMI	41	-2322.3159	4908.6452	0.0000	1.0000
SYMIG	42	-2320.3358	4911.1244	0.0000	1.0000
SYM	40	-2328.8249	4915.2238	0.0000	1.0000
F81G	39	-2351.8607	4954.8560	0.0000	1.0000
F81I	39	-2353.3092	4957.7531	0.0000	1.0000
F81IG	40	-2351.8607	4961.2955	0.0000	1.0000
F81	38	-2358.7407	4962.1768	0.0000	1.0000
JC69G	36	-2365.5995	4963.0155	0.0000	1.0000
JC69I	36	-2366.9839	4965.7844	0.0000	1.0000
JC69IG	37	-2365.5995	4969.4549	0.0000	1.0000
JC69	35	-2372.6029	4970.5831	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/chr11_3426.phylip = 1 - 626;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3426.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3426.phylip = 1 - 626;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3426.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;


[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/chr11_3426.phylip = 1 - 626;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3426.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

