
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:48 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_10340.phylip" (19 taxa, 526 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	-2363.7119	4823.6566	0.7257	0.7257
GTRIG	45	-2363.7118	4826.0486	0.2194	0.9451
HKYG	40	-2371.6444	4830.0516	0.0297	0.9748
GTRI	44	-2367.5814	4831.3957	0.0151	0.9899
HKYIG	41	-2371.6443	4832.4044	0.0091	0.9991
HKYI	40	-2375.0875	4836.9378	0.0009	1.0000
GTR	43	-2392.5023	4878.8552	0.0000	1.0000
K2PG	37	-2401.0128	4881.7879	0.0000	1.0000
HKY	39	-2399.1888	4882.7973	0.0000	1.0000
K2PIG	38	-2401.0127	4884.1116	0.0000	1.0000
SYMG	41	-2397.8421	4884.8000	0.0000	1.0000
SYMIG	42	-2397.8421	4887.1624	0.0000	1.0000
K2PI	37	-2404.9966	4889.7554	0.0000	1.0000
SYMI	41	-2401.9544	4893.0245	0.0000	1.0000
K2P	36	-2428.6004	4934.6486	0.0000	1.0000
SYM	40	-2425.4512	4937.6652	0.0000	1.0000
F81G	39	-2443.7427	4971.9051	0.0000	1.0000
F81IG	40	-2443.7428	4974.2484	0.0000	1.0000
F81I	39	-2447.3234	4979.0665	0.0000	1.0000
JC69G	36	-2463.7658	5004.9795	0.0000	1.0000
JC69IG	37	-2463.7659	5007.2941	0.0000	1.0000
JC69I	36	-2467.9253	5013.2985	0.0000	1.0000
F81	38	-2469.6623	5021.4108	0.0000	1.0000
JC69	35	-2490.2719	5055.6867	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2363.7119	4815.4238	0.7061	0.7061
GTRIG	45	-2363.7118	4817.4236	0.2598	0.9659
GTRI	44	-2367.5814	4823.1628	0.0147	0.9806
HKYG	40	-2371.6444	4823.2887	0.0138	0.9945
HKYIG	41	-2371.6443	4825.2887	0.0051	0.9996
HKYI	40	-2375.0875	4830.1750	0.0004	1.0000
GTR	43	-2392.5023	4871.0046	0.0000	1.0000
K2PG	37	-2401.0128	4876.0256	0.0000	1.0000
HKY	39	-2399.1888	4876.3776	0.0000	1.0000
SYMG	41	-2397.8421	4877.6843	0.0000	1.0000
K2PIG	38	-2401.0127	4878.0253	0.0000	1.0000
SYMIG	42	-2397.8421	4879.6842	0.0000	1.0000
K2PI	37	-2404.9966	4883.9931	0.0000	1.0000
SYMI	41	-2401.9544	4885.9088	0.0000	1.0000
K2P	36	-2428.6004	4929.2008	0.0000	1.0000
SYM	40	-2425.4512	4930.9023	0.0000	1.0000
F81G	39	-2443.7427	4965.4854	0.0000	1.0000
F81IG	40	-2443.7428	4967.4855	0.0000	1.0000
F81I	39	-2447.3234	4972.6468	0.0000	1.0000
JC69G	36	-2463.7658	4999.5317	0.0000	1.0000
JC69IG	37	-2463.7659	5001.5318	0.0000	1.0000
JC69I	36	-2467.9253	5007.8506	0.0000	1.0000
F81	38	-2469.6623	5015.3246	0.0000	1.0000
JC69	35	-2490.2719	5050.5438	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2371.6444	4993.9007	0.9206	0.9206
HKYIG	41	-2371.6443	5000.1660	0.0401	0.9607
HKYI	40	-2375.0875	5000.7870	0.0294	0.9901
GTRG	44	-2363.7119	5003.0971	0.0093	0.9994
GTRIG	45	-2363.7118	5009.3622	0.0004	0.9998
GTRI	44	-2367.5814	5010.8361	0.0002	1.0000
K2PG	37	-2401.0128	5033.8417	0.0000	1.0000
K2PIG	38	-2401.0127	5040.1068	0.0000	1.0000
K2PI	37	-2404.9966	5041.8093	0.0000	1.0000
HKY	39	-2399.1888	5042.7243	0.0000	1.0000
SYMG	41	-2397.8421	5052.5616	0.0000	1.0000
GTR	43	-2392.5023	5054.4125	0.0000	1.0000
SYMIG	42	-2397.8421	5058.8268	0.0000	1.0000
SYMI	41	-2401.9544	5060.7861	0.0000	1.0000
K2P	36	-2428.6004	5082.7516	0.0000	1.0000
SYM	40	-2425.4512	5101.5144	0.0000	1.0000
F81G	39	-2443.7427	5131.8321	0.0000	1.0000
F81IG	40	-2443.7428	5138.0976	0.0000	1.0000
F81I	39	-2447.3234	5138.9935	0.0000	1.0000
JC69G	36	-2463.7658	5153.0825	0.0000	1.0000
JC69IG	37	-2463.7659	5159.3479	0.0000	1.0000
JC69I	36	-2467.9253	5161.4015	0.0000	1.0000
F81	38	-2469.6623	5177.4060	0.0000	1.0000
JC69	35	-2490.2719	5199.8293	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_10340.phylip = 1 - 526;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10340.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_10340.phylip = 1 - 526;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10340.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_10340.phylip = 1 - 526;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10340.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

