
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:45 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_16820.phylip" (19 taxa, 633 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
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
HKYIG	41	-2407.6172	4903.0619	0.5400	0.5400
HKYG	40	-2409.0211	4903.5828	0.4162	0.9562
GTRIG	45	-2406.2340	4909.5208	0.0214	0.9775
GTRG	44	-2407.5846	4909.9039	0.0176	0.9952
HKYI	40	-2413.8779	4913.2964	0.0032	0.9984
K2PIG	38	-2417.7169	4916.4238	0.0007	0.9991
K2PG	37	-2418.8526	4916.4312	0.0007	0.9998
GTRI	44	-2412.3458	4919.4264	0.0002	0.9999
SYMG	41	-2417.3301	4922.4875	0.0000	1.0000
SYMIG	42	-2416.2514	4922.6249	0.0000	1.0000
K2PI	37	-2422.6843	4924.0947	0.0000	1.0000
SYMI	41	-2420.4217	4928.6708	0.0000	1.0000
F81G	39	-2469.6051	5022.4715	0.0000	1.0000
F81IG	40	-2468.8254	5023.1914	0.0000	1.0000
F81I	39	-2473.0209	5029.3032	0.0000	1.0000
JC69G	36	-2477.5664	5031.6027	0.0000	1.0000
JC69IG	37	-2477.0910	5032.9080	0.0000	1.0000
JC69I	36	-2480.8018	5038.0734	0.0000	1.0000
HKY	39	-2490.0167	5063.2948	0.0000	1.0000
GTR	43	-2488.4964	5069.4173	0.0000	1.0000
K2P	36	-2499.4513	5075.3724	0.0000	1.0000
SYM	40	-2498.1067	5081.7538	0.0000	1.0000
F81	38	-2547.0675	5175.1249	0.0000	1.0000
JC69	35	-2554.6117	5183.4444	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-2407.6172	4897.2345	0.5557	0.5557
HKYG	40	-2409.0211	4898.0423	0.3710	0.9268
GTRIG	45	-2406.2340	4902.4679	0.0406	0.9673
GTRG	44	-2407.5846	4903.1692	0.0286	0.9959
HKYI	40	-2413.8779	4907.7558	0.0029	0.9988
K2PIG	38	-2417.7169	4911.4339	0.0005	0.9993
K2PG	37	-2418.8526	4911.7052	0.0004	0.9997
GTRI	44	-2412.3458	4912.6917	0.0002	0.9999
SYMIG	42	-2416.2514	4916.5029	0.0000	1.0000
SYMG	41	-2417.3301	4916.6601	0.0000	1.0000
K2PI	37	-2422.6843	4919.3686	0.0000	1.0000
SYMI	41	-2420.4217	4922.8434	0.0000	1.0000
F81G	39	-2469.6051	5017.2101	0.0000	1.0000
F81IG	40	-2468.8254	5017.6508	0.0000	1.0000
F81I	39	-2473.0209	5024.0418	0.0000	1.0000
JC69G	36	-2477.5664	5027.1329	0.0000	1.0000
JC69IG	37	-2477.0910	5028.1820	0.0000	1.0000
JC69I	36	-2480.8018	5033.6036	0.0000	1.0000
HKY	39	-2490.0167	5058.0335	0.0000	1.0000
GTR	43	-2488.4964	5062.9929	0.0000	1.0000
K2P	36	-2499.4513	5070.9026	0.0000	1.0000
SYM	40	-2498.1067	5076.2133	0.0000	1.0000
F81	38	-2547.0675	5170.1350	0.0000	1.0000
JC69	35	-2554.6117	5179.2233	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2409.0211	5076.0611	0.4652	0.4652
K2PG	37	-2418.8526	5076.3726	0.3981	0.8632
HKYIG	41	-2407.6172	5079.7037	0.0753	0.9385
K2PIG	38	-2417.7169	5080.5518	0.0493	0.9877
K2PI	37	-2422.6843	5084.0360	0.0086	0.9964
HKYI	40	-2413.8779	5085.7747	0.0036	1.0000
GTRG	44	-2407.5846	5098.9899	0.0000	1.0000
SYMG	41	-2417.3301	5099.1294	0.0000	1.0000
GTRIG	45	-2406.2340	5102.7391	0.0000	1.0000
SYMIG	42	-2416.2514	5103.4226	0.0000	1.0000
SYMI	41	-2420.4217	5105.3126	0.0000	1.0000
GTRI	44	-2412.3458	5108.5124	0.0000	1.0000
JC69G	36	-2477.5664	5187.3498	0.0000	1.0000
F81G	39	-2469.6051	5190.7784	0.0000	1.0000
JC69IG	37	-2477.0910	5192.8494	0.0000	1.0000
JC69I	36	-2480.8018	5193.8205	0.0000	1.0000
F81IG	40	-2468.8254	5195.6696	0.0000	1.0000
F81I	39	-2473.0209	5197.6101	0.0000	1.0000
K2P	36	-2499.4513	5231.1195	0.0000	1.0000
HKY	39	-2490.0167	5231.6018	0.0000	1.0000
SYM	40	-2498.1067	5254.2321	0.0000	1.0000
GTR	43	-2488.4964	5254.3631	0.0000	1.0000
JC69	35	-2554.6117	5334.9898	0.0000	1.0000
F81	38	-2547.0675	5339.2529	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_16820.phylip = 1 - 633;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_16820.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_16820.phylip = 1 - 633;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_16820.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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_16820.phylip = 1 - 633;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_16820.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

