
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:42 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/chr20_5193.phylip" (19 taxa, 472 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-2364.9055	4827.0851	0.6295	0.6295
GTRIG	45	-2364.3166	4828.3515	0.3342	0.9637
SYMG	41	-2371.9639	4833.9372	0.0205	0.9842
SYMIG	42	-2371.0331	4834.4858	0.0156	0.9998
GTRI	44	-2374.0413	4845.3566	0.0001	0.9998
K2PIG	38	-2381.4731	4845.7915	0.0001	0.9999
HKYIG	41	-2378.0431	4846.0956	0.0000	0.9999
K2PG	37	-2383.2280	4846.9353	0.0000	1.0000
HKYG	40	-2379.8974	4847.4050	0.0000	1.0000
SYMI	41	-2379.7645	4849.5383	0.0000	1.0000
K2PI	37	-2392.9882	4866.4557	0.0000	1.0000
HKYI	40	-2389.7627	4867.1355	0.0000	1.0000
F81G	39	-2454.6944	4994.6111	0.0000	1.0000
F81IG	40	-2454.3160	4996.2422	0.0000	1.0000
JC69G	36	-2461.0978	5000.3198	0.0000	1.0000
JC69IG	37	-2460.4841	5001.4475	0.0000	1.0000
F81I	39	-2460.4999	5006.2219	0.0000	1.0000
JC69I	36	-2466.7753	5011.6746	0.0000	1.0000
GTR	43	-2467.7228	5030.2867	0.0000	1.0000
SYM	40	-2478.3947	5044.3995	0.0000	1.0000
HKY	39	-2493.2320	5071.6861	0.0000	1.0000
K2P	36	-2498.5159	5075.1559	0.0000	1.0000
F81	38	-2558.9734	5200.7920	0.0000	1.0000
JC69	35	-2565.4369	5206.6537	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2364.9055	4817.8111	0.5894	0.5894
GTRIG	45	-2364.3166	4818.6332	0.3908	0.9802
SYMG	41	-2371.9639	4825.9279	0.0102	0.9904
SYMIG	42	-2371.0331	4826.0663	0.0095	0.9999
GTRI	44	-2374.0413	4836.0826	0.0001	0.9999
HKYIG	41	-2378.0431	4838.0863	0.0000	1.0000
K2PIG	38	-2381.4731	4838.9463	0.0000	1.0000
HKYG	40	-2379.8974	4839.7948	0.0000	1.0000
K2PG	37	-2383.2280	4840.4560	0.0000	1.0000
SYMI	41	-2379.7645	4841.5290	0.0000	1.0000
HKYI	40	-2389.7627	4859.5253	0.0000	1.0000
K2PI	37	-2392.9882	4859.9765	0.0000	1.0000
F81G	39	-2454.6944	4987.3888	0.0000	1.0000
F81IG	40	-2454.3160	4988.6320	0.0000	1.0000
JC69G	36	-2461.0978	4994.1956	0.0000	1.0000
JC69IG	37	-2460.4841	4994.9682	0.0000	1.0000
F81I	39	-2460.4999	4998.9997	0.0000	1.0000
JC69I	36	-2466.7753	5005.5505	0.0000	1.0000
GTR	43	-2467.7228	5021.4455	0.0000	1.0000
SYM	40	-2478.3947	5036.7893	0.0000	1.0000
HKY	39	-2493.2320	5064.4639	0.0000	1.0000
K2P	36	-2498.5159	5069.0318	0.0000	1.0000
F81	38	-2558.9734	5193.9467	0.0000	1.0000
JC69	35	-2565.4369	5200.8738	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2383.2280	4994.2642	0.5870	0.5870
SYMG	41	-2371.9639	4996.3640	0.2054	0.7924
K2PIG	38	-2381.4731	4996.9115	0.1562	0.9486
SYMIG	42	-2371.0331	5000.6594	0.0240	0.9726
GTRG	44	-2364.9055	5000.7181	0.0233	0.9959
GTRIG	45	-2364.3166	5005.6972	0.0019	0.9978
HKYG	40	-2379.8974	5006.0739	0.0016	0.9994
HKYIG	41	-2378.0431	5008.5224	0.0005	0.9999
SYMI	41	-2379.7645	5011.9652	0.0001	1.0000
K2PI	37	-2392.9882	5013.7847	0.0000	1.0000
GTRI	44	-2374.0413	5018.9897	0.0000	1.0000
HKYI	40	-2389.7627	5025.8045	0.0000	1.0000
JC69G	36	-2461.0978	5143.8469	0.0000	1.0000
JC69IG	37	-2460.4841	5148.7764	0.0000	1.0000
F81G	39	-2454.6944	5149.5110	0.0000	1.0000
F81IG	40	-2454.3160	5154.9112	0.0000	1.0000
JC69I	36	-2466.7753	5155.2017	0.0000	1.0000
F81I	39	-2460.4999	5161.1219	0.0000	1.0000
GTR	43	-2467.7228	5200.1956	0.0000	1.0000
SYM	40	-2478.3947	5203.0685	0.0000	1.0000
K2P	36	-2498.5159	5218.6830	0.0000	1.0000
HKY	39	-2493.2320	5226.5861	0.0000	1.0000
JC69	35	-2565.4369	5346.3681	0.0000	1.0000
F81	38	-2558.9734	5351.9119	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/chr20_5193.phylip = 1 - 472;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr20_5193.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/chr20_5193.phylip = 1 - 472;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr20_5193.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr20_5193.phylip = 1 - 472;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr20_5193.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

