
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:57 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/chr3_300.phylip" (19 taxa, 642 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	-2333.9492	4762.5315	0.6914	0.6914
GTRIG	45	-2333.8510	4764.6483	0.2399	0.9314
GTRI	44	-2336.2772	4767.1876	0.0674	0.9988
HKYG	40	-2345.2410	4775.9396	0.0008	0.9996
HKYIG	41	-2345.0619	4777.8637	0.0003	0.9999
HKYI	40	-2347.8629	4781.1833	0.0001	1.0000
K2PG	37	-2376.1539	4830.9633	0.0000	1.0000
K2PIG	38	-2375.9046	4832.7245	0.0000	1.0000
SYMG	41	-2373.9140	4835.5679	0.0000	1.0000
K2PI	37	-2378.9065	4836.4687	0.0000	1.0000
SYMIG	42	-2373.6729	4837.3758	0.0000	1.0000
SYMI	41	-2376.3476	4840.4351	0.0000	1.0000
GTR	43	-2376.1413	4844.6103	0.0000	1.0000
HKY	39	-2386.5575	4856.2977	0.0000	1.0000
F81G	39	-2388.2729	4859.7286	0.0000	1.0000
F81IG	40	-2388.1450	4861.7475	0.0000	1.0000
F81I	39	-2390.3007	4863.7840	0.0000	1.0000
JC69G	36	-2415.1388	4906.6809	0.0000	1.0000
JC69IG	37	-2414.9639	4908.5834	0.0000	1.0000
JC69I	36	-2417.6537	4911.7107	0.0000	1.0000
K2P	36	-2419.6329	4915.6691	0.0000	1.0000
SYM	40	-2417.0055	4919.4686	0.0000	1.0000
F81	38	-2428.9051	4938.7257	0.0000	1.0000
JC69	35	-2456.9781	4988.1147	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2333.9492	4755.8983	0.6647	0.6647
GTRIG	45	-2333.8510	4757.7020	0.2698	0.9345
GTRI	44	-2336.2772	4760.5544	0.0648	0.9993
HKYG	40	-2345.2410	4770.4820	0.0005	0.9998
HKYIG	41	-2345.0619	4772.1237	0.0002	1.0000
HKYI	40	-2347.8629	4775.7257	0.0000	1.0000
K2PG	37	-2376.1539	4826.3077	0.0000	1.0000
K2PIG	38	-2375.9046	4827.8091	0.0000	1.0000
SYMG	41	-2373.9140	4829.8279	0.0000	1.0000
SYMIG	42	-2373.6729	4831.3457	0.0000	1.0000
K2PI	37	-2378.9065	4831.8131	0.0000	1.0000
SYMI	41	-2376.3476	4834.6951	0.0000	1.0000
GTR	43	-2376.1413	4838.2825	0.0000	1.0000
HKY	39	-2386.5575	4851.1150	0.0000	1.0000
F81G	39	-2388.2729	4854.5458	0.0000	1.0000
F81IG	40	-2388.1450	4856.2900	0.0000	1.0000
F81I	39	-2390.3007	4858.6013	0.0000	1.0000
JC69G	36	-2415.1388	4902.2776	0.0000	1.0000
JC69IG	37	-2414.9639	4903.9277	0.0000	1.0000
JC69I	36	-2417.6537	4907.3074	0.0000	1.0000
K2P	36	-2419.6329	4911.2658	0.0000	1.0000
SYM	40	-2417.0055	4914.0110	0.0000	1.0000
F81	38	-2428.9051	4933.8103	0.0000	1.0000
JC69	35	-2456.9781	4983.9563	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2345.2410	4949.0656	0.7453	0.7453
GTRG	44	-2333.9492	4952.3402	0.1450	0.8902
HKYI	40	-2347.8629	4954.3093	0.0542	0.9444
HKYIG	41	-2345.0619	4955.1718	0.0352	0.9796
GTRI	44	-2336.2772	4956.9963	0.0141	0.9937
GTRIG	45	-2333.8510	4958.6085	0.0063	1.0000
K2PG	37	-2376.1539	4991.4975	0.0000	1.0000
K2PI	37	-2378.9065	4997.0028	0.0000	1.0000
K2PIG	38	-2375.9046	4997.4635	0.0000	1.0000
SYMG	41	-2373.9140	5012.8760	0.0000	1.0000
SYMI	41	-2376.3476	5017.7433	0.0000	1.0000
SYMIG	42	-2373.6729	5018.8584	0.0000	1.0000
HKY	39	-2386.5575	5025.2339	0.0000	1.0000
F81G	39	-2388.2729	5028.6648	0.0000	1.0000
GTR	43	-2376.1413	5030.2598	0.0000	1.0000
F81I	39	-2390.3007	5032.7203	0.0000	1.0000
F81IG	40	-2388.1450	5034.8735	0.0000	1.0000
JC69G	36	-2415.1388	5063.0028	0.0000	1.0000
JC69I	36	-2417.6537	5068.0325	0.0000	1.0000
JC69IG	37	-2414.9639	5069.1175	0.0000	1.0000
K2P	36	-2419.6329	5071.9909	0.0000	1.0000
SYM	40	-2417.0055	5092.5946	0.0000	1.0000
F81	38	-2428.9051	5103.4646	0.0000	1.0000
JC69	35	-2456.9781	5140.2169	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/chr3_300.phylip = 1 - 642;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_300.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/chr3_300.phylip = 1 - 642;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_300.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/chr3_300.phylip = 1 - 642;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_300.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

