
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:03 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/chr5_10854.phylip" (19 taxa, 874 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	-4823.6033	9739.9834	0.5365	0.5365
GTRIG	45	-4822.7840	9740.5681	0.4005	0.9370
HKYIG	41	-4830.0244	9746.1883	0.0241	0.9611
HKYG	40	-4831.3368	9746.6112	0.0195	0.9807
GTRI	44	-4827.1216	9747.0200	0.0159	0.9966
HKYI	40	-4833.0761	9750.0897	0.0034	1.0000
K2PIG	38	-4861.7371	9803.0240	0.0000	1.0000
K2PG	37	-4863.4821	9804.3279	0.0000	1.0000
K2PI	37	-4864.2415	9805.8467	0.0000	1.0000
SYMIG	42	-4861.1902	9810.7269	0.0000	1.0000
SYMG	41	-4862.9664	9812.0723	0.0000	1.0000
SYMI	41	-4863.6235	9813.3864	0.0000	1.0000
GTR	43	-4880.2839	9851.1268	0.0000	1.0000
HKY	39	-4887.0637	9855.8685	0.0000	1.0000
K2P	36	-4921.2907	9917.7642	0.0000	1.0000
SYM	40	-4919.9719	9923.8814	0.0000	1.0000
F81IG	40	-4981.2235	10046.3847	0.0000	1.0000
F81I	39	-4982.5322	10046.8054	0.0000	1.0000
F81G	39	-4983.6383	10049.0175	0.0000	1.0000
JC69IG	37	-5005.7204	10088.8045	0.0000	1.0000
JC69I	36	-5006.8552	10088.8932	0.0000	1.0000
JC69G	36	-5008.4188	10092.0205	0.0000	1.0000
F81	38	-5034.5625	10148.6746	0.0000	1.0000
JC69	35	-5059.8440	10192.6951	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4823.6033	9735.2066	0.5195	0.5195
GTRIG	45	-4822.7840	9735.5681	0.4336	0.9530
HKYIG	41	-4830.0244	9742.0489	0.0170	0.9700
GTRI	44	-4827.1216	9742.2432	0.0154	0.9854
HKYG	40	-4831.3368	9742.6736	0.0124	0.9978
HKYI	40	-4833.0761	9746.1521	0.0022	1.0000
K2PIG	38	-4861.7371	9799.4743	0.0000	1.0000
K2PG	37	-4863.4821	9800.9643	0.0000	1.0000
K2PI	37	-4864.2415	9802.4831	0.0000	1.0000
SYMIG	42	-4861.1902	9806.3804	0.0000	1.0000
SYMG	41	-4862.9664	9807.9329	0.0000	1.0000
SYMI	41	-4863.6235	9809.2470	0.0000	1.0000
GTR	43	-4880.2839	9846.5678	0.0000	1.0000
HKY	39	-4887.0637	9852.1275	0.0000	1.0000
K2P	36	-4921.2907	9914.5814	0.0000	1.0000
SYM	40	-4919.9719	9919.9438	0.0000	1.0000
F81IG	40	-4981.2235	10042.4471	0.0000	1.0000
F81I	39	-4982.5322	10043.0644	0.0000	1.0000
F81G	39	-4983.6383	10045.2765	0.0000	1.0000
JC69IG	37	-5005.7204	10085.4408	0.0000	1.0000
JC69I	36	-5006.8552	10085.7104	0.0000	1.0000
JC69G	36	-5008.4188	10088.8377	0.0000	1.0000
F81	38	-5034.5625	10145.1249	0.0000	1.0000
JC69	35	-5059.8440	10189.6879	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4831.3368	9933.5968	0.7665	0.7665
HKYI	40	-4833.0761	9937.0753	0.1346	0.9011
HKYIG	41	-4830.0244	9937.7452	0.0963	0.9975
GTRG	44	-4823.6033	9945.2221	0.0023	0.9998
GTRIG	45	-4822.7840	9950.3567	0.0002	0.9999
GTRI	44	-4827.1216	9952.2587	0.0001	1.0000
K2PG	37	-4863.4821	9977.5683	0.0000	1.0000
K2PI	37	-4864.2415	9979.0871	0.0000	1.0000
K2PIG	38	-4861.7371	9980.8514	0.0000	1.0000
SYMG	41	-4862.9664	10003.6292	0.0000	1.0000
SYMI	41	-4863.6235	10004.9433	0.0000	1.0000
SYMIG	42	-4861.1902	10006.8497	0.0000	1.0000
HKY	39	-4887.0637	10038.2776	0.0000	1.0000
GTR	43	-4880.2839	10051.8103	0.0000	1.0000
K2P	36	-4921.2907	10086.4123	0.0000	1.0000
SYM	40	-4919.9719	10110.8671	0.0000	1.0000
F81I	39	-4982.5322	10229.2145	0.0000	1.0000
F81G	39	-4983.6383	10231.4267	0.0000	1.0000
F81IG	40	-4981.2235	10233.3703	0.0000	1.0000
JC69I	36	-5006.8552	10257.5413	0.0000	1.0000
JC69G	36	-5008.4188	10260.6686	0.0000	1.0000
JC69IG	37	-5005.7204	10262.0448	0.0000	1.0000
F81	38	-5034.5625	10326.5020	0.0000	1.0000
JC69	35	-5059.8440	10356.7458	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/chr5_10854.phylip = 1 - 874;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10854.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/chr5_10854.phylip = 1 - 874;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10854.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/chr5_10854.phylip = 1 - 874;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10854.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

