
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:45 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/chr7_10552.phylip" (19 taxa, 667 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	-2369.7594	4833.8853	0.4823	0.4823
GTRIG	45	-2369.4237	4835.5140	0.2136	0.6959
HKYG	40	-2375.1851	4835.6097	0.2036	0.8995
HKYIG	41	-2374.8557	4837.2218	0.0909	0.9904
GTRI	44	-2374.1788	4842.7242	0.0058	0.9962
HKYI	40	-2379.4526	4844.1448	0.0029	0.9991
SYMG	41	-2380.0778	4847.6660	0.0005	0.9996
SYMIG	42	-2379.8749	4849.5383	0.0002	0.9998
K2PG	37	-2385.7713	4850.0131	0.0002	0.9999
K2PIG	38	-2385.5219	4851.7635	0.0001	1.0000
SYMI	41	-2383.5596	4854.6296	0.0000	1.0000
K2PI	37	-2389.6848	4857.8401	0.0000	1.0000
F81G	39	-2415.4385	4913.8530	0.0000	1.0000
F81IG	40	-2415.0264	4915.2924	0.0000	1.0000
GTR	43	-2413.7112	4919.4962	0.0000	1.0000
HKY	39	-2418.2744	4919.5249	0.0000	1.0000
F81I	39	-2419.7912	4922.5586	0.0000	1.0000
JC69G	36	-2423.5640	4923.3566	0.0000	1.0000
JC69IG	37	-2423.2209	4924.9124	0.0000	1.0000
SYM	40	-2422.8882	4931.0160	0.0000	1.0000
JC69I	36	-2427.5408	4931.3101	0.0000	1.0000
K2P	36	-2427.8648	4931.9583	0.0000	1.0000
F81	38	-2457.9793	4996.6783	0.0000	1.0000
JC69	35	-2465.3579	5004.7095	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2369.7594	4827.5188	0.5279	0.5279
GTRIG	45	-2369.4237	4828.8473	0.2717	0.7995
HKYG	40	-2375.1851	4830.3701	0.1269	0.9264
HKYIG	41	-2374.8557	4831.7114	0.0649	0.9913
GTRI	44	-2374.1788	4836.3577	0.0064	0.9976
HKYI	40	-2379.4526	4838.9052	0.0018	0.9994
SYMG	41	-2380.0778	4842.1556	0.0004	0.9997
SYMIG	42	-2379.8749	4843.7499	0.0002	0.9999
K2PG	37	-2385.7713	4845.5425	0.0001	1.0000
K2PIG	38	-2385.5219	4847.0438	0.0000	1.0000
SYMI	41	-2383.5596	4849.1192	0.0000	1.0000
K2PI	37	-2389.6848	4853.3695	0.0000	1.0000
F81G	39	-2415.4385	4908.8770	0.0000	1.0000
F81IG	40	-2415.0264	4910.0528	0.0000	1.0000
GTR	43	-2413.7112	4913.4224	0.0000	1.0000
HKY	39	-2418.2744	4914.5488	0.0000	1.0000
F81I	39	-2419.7912	4917.5825	0.0000	1.0000
JC69G	36	-2423.5640	4919.1280	0.0000	1.0000
JC69IG	37	-2423.2209	4920.4418	0.0000	1.0000
SYM	40	-2422.8882	4925.7764	0.0000	1.0000
JC69I	36	-2427.5408	4927.0815	0.0000	1.0000
K2P	36	-2427.8648	4927.7297	0.0000	1.0000
F81	38	-2457.9793	4991.9586	0.0000	1.0000
JC69	35	-2465.3579	5000.7158	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2375.1851	5010.4817	0.6518	0.6518
K2PG	37	-2385.7713	5012.1458	0.2837	0.9355
HKYIG	41	-2374.8557	5016.3258	0.0351	0.9705
K2PIG	38	-2385.5219	5018.1498	0.0141	0.9846
HKYI	40	-2379.4526	5019.0168	0.0091	0.9938
K2PI	37	-2389.6848	5019.9728	0.0057	0.9994
GTRG	44	-2369.7594	5025.6415	0.0003	0.9998
SYMG	41	-2380.0778	5026.7700	0.0002	1.0000
GTRIG	45	-2369.4237	5031.4729	0.0000	1.0000
SYMIG	42	-2379.8749	5032.8671	0.0000	1.0000
SYMI	41	-2383.5596	5033.7336	0.0000	1.0000
GTRI	44	-2374.1788	5034.4804	0.0000	1.0000
JC69G	36	-2423.5640	5081.2284	0.0000	1.0000
F81G	39	-2415.4385	5084.4858	0.0000	1.0000
JC69IG	37	-2423.2209	5087.0450	0.0000	1.0000
JC69I	36	-2427.5408	5089.1819	0.0000	1.0000
K2P	36	-2427.8648	5089.8301	0.0000	1.0000
HKY	39	-2418.2744	5090.1576	0.0000	1.0000
F81IG	40	-2415.0264	5090.1644	0.0000	1.0000
F81I	39	-2419.7912	5093.1913	0.0000	1.0000
SYM	40	-2422.8882	5105.8880	0.0000	1.0000
GTR	43	-2413.7112	5107.0424	0.0000	1.0000
JC69	35	-2465.3579	5158.3135	0.0000	1.0000
F81	38	-2457.9793	5163.0646	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/chr7_10552.phylip = 1 - 667;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10552.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/chr7_10552.phylip = 1 - 667;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10552.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/chr7_10552.phylip = 1 - 667;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10552.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

