
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:27 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/chr11_3210.phylip" (19 taxa, 1153 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
Minimum BIC  model: HKYI


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
GTRI	44	-2717.5067	5526.5874	0.4577	0.4577
GTRG	44	-2717.6415	5526.8571	0.4000	0.8577
GTRIG	45	-2717.6413	5529.0224	0.1355	0.9932
HKYI	40	-2726.7850	5536.5197	0.0032	0.9964
HKYG	40	-2726.9443	5536.8382	0.0027	0.9991
HKYIG	41	-2726.9441	5538.9882	0.0009	1.0000
GTR	43	-2739.6174	5568.6468	0.0000	1.0000
HKY	39	-2747.2362	5575.2756	0.0000	1.0000
K2PI	37	-2766.1877	5608.8974	0.0000	1.0000
K2PG	37	-2766.3526	5609.2272	0.0000	1.0000
SYMI	41	-2762.3217	5609.7433	0.0000	1.0000
SYMG	41	-2762.5117	5610.1233	0.0000	1.0000
K2PIG	38	-2766.3525	5611.3657	0.0000	1.0000
SYMIG	42	-2762.5115	5612.2771	0.0000	1.0000
F81I	39	-2766.4445	5613.6922	0.0000	1.0000
F81G	39	-2766.5533	5613.9098	0.0000	1.0000
F81IG	40	-2766.5531	5616.0559	0.0000	1.0000
K2P	36	-2784.6527	5643.6924	0.0000	1.0000
SYM	40	-2780.8954	5644.7405	0.0000	1.0000
F81	38	-2784.6036	5647.8678	0.0000	1.0000
JC69I	36	-2800.7217	5675.8305	0.0000	1.0000
JC69G	36	-2800.8322	5676.0515	0.0000	1.0000
JC69IG	37	-2800.8320	5678.1859	0.0000	1.0000
JC69	35	-2818.2899	5708.8359	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-2717.5067	5523.0134	0.4532	0.4532
GTRG	44	-2717.6415	5523.2831	0.3960	0.8493
GTRIG	45	-2717.6413	5525.2826	0.1457	0.9950
HKYI	40	-2726.7850	5533.5701	0.0023	0.9973
HKYG	40	-2726.9443	5533.8886	0.0020	0.9993
HKYIG	41	-2726.9441	5535.8883	0.0007	1.0000
GTR	43	-2739.6174	5565.2347	0.0000	1.0000
HKY	39	-2747.2362	5572.4724	0.0000	1.0000
K2PI	37	-2766.1877	5606.3754	0.0000	1.0000
SYMI	41	-2762.3217	5606.6434	0.0000	1.0000
K2PG	37	-2766.3526	5606.7053	0.0000	1.0000
SYMG	41	-2762.5117	5607.0234	0.0000	1.0000
K2PIG	38	-2766.3525	5608.7050	0.0000	1.0000
SYMIG	42	-2762.5115	5609.0230	0.0000	1.0000
F81I	39	-2766.4445	5610.8890	0.0000	1.0000
F81G	39	-2766.5533	5611.1066	0.0000	1.0000
F81IG	40	-2766.5531	5613.1062	0.0000	1.0000
K2P	36	-2784.6527	5641.3053	0.0000	1.0000
SYM	40	-2780.8954	5641.7909	0.0000	1.0000
F81	38	-2784.6036	5645.2071	0.0000	1.0000
JC69I	36	-2800.7217	5673.4434	0.0000	1.0000
JC69G	36	-2800.8322	5673.6644	0.0000	1.0000
JC69IG	37	-2800.8320	5675.6639	0.0000	1.0000
JC69	35	-2818.2899	5706.5799	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-2726.7850	5735.5750	0.5282	0.5282
HKYG	40	-2726.9443	5735.8935	0.4504	0.9787
HKYIG	41	-2726.9441	5742.9433	0.0133	0.9919
GTRI	44	-2717.5067	5745.2188	0.0043	0.9962
GTRG	44	-2717.6415	5745.4885	0.0037	0.9999
GTRIG	45	-2717.6413	5752.5381	0.0001	1.0000
HKY	39	-2747.2362	5769.4271	0.0000	1.0000
GTR	43	-2739.6174	5782.3900	0.0000	1.0000
K2PI	37	-2766.1877	5793.2299	0.0000	1.0000
K2PG	37	-2766.3526	5793.5598	0.0000	1.0000
K2PIG	38	-2766.3525	5800.6097	0.0000	1.0000
F81I	39	-2766.4445	5807.8438	0.0000	1.0000
F81G	39	-2766.5533	5808.0614	0.0000	1.0000
SYMI	41	-2762.3217	5813.6984	0.0000	1.0000
SYMG	41	-2762.5117	5814.0784	0.0000	1.0000
F81IG	40	-2766.5531	5815.1111	0.0000	1.0000
SYMIG	42	-2762.5115	5821.1282	0.0000	1.0000
K2P	36	-2784.6527	5823.1098	0.0000	1.0000
F81	38	-2784.6036	5837.1118	0.0000	1.0000
SYM	40	-2780.8954	5843.7958	0.0000	1.0000
JC69I	36	-2800.7217	5855.2478	0.0000	1.0000
JC69G	36	-2800.8322	5855.4688	0.0000	1.0000
JC69IG	37	-2800.8320	5862.5185	0.0000	1.0000
JC69	35	-2818.2899	5883.3342	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3210.phylip = 1 - 1153;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3210.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3210.phylip = 1 - 1153;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3210.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3210.phylip = 1 - 1153;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3210.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

