
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:26 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/chr6_3170.phylip" (19 taxa, 900 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	-4850.0229	9792.6774	0.6260	0.6260
GTRIG	45	-4849.4625	9793.7728	0.3620	0.9879
SYMIG	42	-4856.2129	9800.6406	0.0117	0.9996
SYMG	41	-4861.0807	9808.1754	0.0003	0.9999
K2PG	37	-4866.8920	9811.0461	0.0001	0.9999
K2PIG	38	-4866.4306	9812.3036	0.0000	1.0000
HKYG	40	-4864.9657	9813.7498	0.0000	1.0000
HKYIG	41	-4864.5327	9815.0794	0.0000	1.0000
GTRI	44	-4881.9986	9856.6288	0.0000	1.0000
SYMI	41	-4886.8885	9859.7909	0.0000	1.0000
K2PI	37	-4895.1728	9867.6078	0.0000	1.0000
HKYI	40	-4893.4157	9870.6497	0.0000	1.0000
JC69G	36	-4983.6859	10042.4587	0.0000	1.0000
JC69IG	37	-4983.2252	10043.7126	0.0000	1.0000
F81G	39	-4982.0251	10045.6780	0.0000	1.0000
F81IG	40	-4981.5383	10046.8950	0.0000	1.0000
JC69I	36	-5003.3913	10081.8696	0.0000	1.0000
F81I	39	-5001.8056	10085.2391	0.0000	1.0000
GTR	43	-5074.3224	10239.0653	0.0000	1.0000
SYM	40	-5083.4832	10250.7848	0.0000	1.0000
HKY	39	-5088.9202	10259.4683	0.0000	1.0000
K2P	36	-5092.7444	10260.5756	0.0000	1.0000
JC69	35	-5191.6131	10456.1429	0.0000	1.0000
F81	38	-5189.0141	10457.4707	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4850.0229	9788.0458	0.6025	0.6025
GTRIG	45	-4849.4625	9788.9250	0.3882	0.9906
SYMIG	42	-4856.2129	9796.4259	0.0091	0.9997
SYMG	41	-4861.0807	9804.1614	0.0002	0.9999
K2PG	37	-4866.8920	9807.7839	0.0000	1.0000
K2PIG	38	-4866.4306	9808.8611	0.0000	1.0000
HKYG	40	-4864.9657	9809.9314	0.0000	1.0000
HKYIG	41	-4864.5327	9811.0654	0.0000	1.0000
GTRI	44	-4881.9986	9851.9972	0.0000	1.0000
SYMI	41	-4886.8885	9855.7769	0.0000	1.0000
K2PI	37	-4895.1728	9864.3456	0.0000	1.0000
HKYI	40	-4893.4157	9866.8313	0.0000	1.0000
JC69G	36	-4983.6859	10039.3718	0.0000	1.0000
JC69IG	37	-4983.2252	10040.4504	0.0000	1.0000
F81G	39	-4982.0251	10042.0501	0.0000	1.0000
F81IG	40	-4981.5383	10043.0766	0.0000	1.0000
JC69I	36	-5003.3913	10078.7827	0.0000	1.0000
F81I	39	-5001.8056	10081.6112	0.0000	1.0000
GTR	43	-5074.3224	10234.6448	0.0000	1.0000
SYM	40	-5083.4832	10246.9664	0.0000	1.0000
HKY	39	-5088.9202	10255.8404	0.0000	1.0000
K2P	36	-5092.7444	10257.4887	0.0000	1.0000
JC69	35	-5191.6131	10453.2262	0.0000	1.0000
F81	38	-5189.0141	10454.0282	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-4866.8920	9985.4725	0.9466	0.9466
K2PIG	38	-4866.4306	9991.3521	0.0501	0.9967
SYMIG	42	-4856.2129	9998.1265	0.0017	0.9984
GTRG	44	-4850.0229	9999.3511	0.0009	0.9993
SYMG	41	-4861.0807	10001.0596	0.0004	0.9997
HKYG	40	-4864.9657	10002.0272	0.0002	0.9999
GTRIG	45	-4849.4625	10005.0328	0.0001	1.0000
HKYIG	41	-4864.5327	10007.9636	0.0000	1.0000
K2PI	37	-4895.1728	10042.0342	0.0000	1.0000
SYMI	41	-4886.8885	10052.6751	0.0000	1.0000
HKYI	40	-4893.4157	10058.9271	0.0000	1.0000
GTRI	44	-4881.9986	10063.3025	0.0000	1.0000
JC69G	36	-4983.6859	10212.2580	0.0000	1.0000
JC69IG	37	-4983.2252	10218.1390	0.0000	1.0000
F81G	39	-4982.0251	10229.3435	0.0000	1.0000
F81IG	40	-4981.5383	10235.1724	0.0000	1.0000
JC69I	36	-5003.3913	10251.6689	0.0000	1.0000
F81I	39	-5001.8056	10268.9046	0.0000	1.0000
K2P	36	-5092.7444	10430.3749	0.0000	1.0000
SYM	40	-5083.4832	10439.0622	0.0000	1.0000
GTR	43	-5074.3224	10441.1478	0.0000	1.0000
HKY	39	-5088.9202	10443.1338	0.0000	1.0000
JC69	35	-5191.6131	10621.3100	0.0000	1.0000
F81	38	-5189.0141	10636.5192	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/chr6_3170.phylip = 1 - 900;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3170.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/chr6_3170.phylip = 1 - 900;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3170.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/chr6_3170.phylip = 1 - 900;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3170.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

