
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:17 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_5015.phylip" (19 taxa, 968 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	-2569.3809	5231.0521	0.7308	0.7308
GTRG	44	-2570.8231	5233.9365	0.1728	0.9035
GTRIG	45	-2570.3355	5235.1611	0.0937	0.9972
HKYI	40	-2579.6061	5242.7506	0.0021	0.9993
HKYG	40	-2581.1124	5245.7631	0.0005	0.9998
HKYIG	41	-2580.6973	5247.1137	0.0002	1.0000
SYMG	41	-2587.5887	5260.8967	0.0000	1.0000
SYMIG	42	-2587.2116	5262.3281	0.0000	1.0000
SYMI	41	-2588.4561	5262.6314	0.0000	1.0000
K2PG	37	-2593.5240	5264.0717	0.0000	1.0000
K2PIG	38	-2593.1476	5265.4857	0.0000	1.0000
K2PI	37	-2594.4173	5265.8583	0.0000	1.0000
GTR	43	-2599.4859	5289.0671	0.0000	1.0000
HKY	39	-2608.8645	5299.0911	0.0000	1.0000
SYM	40	-2614.3071	5312.1524	0.0000	1.0000
K2P	36	-2620.2190	5315.2995	0.0000	1.0000
F81G	39	-2623.5857	5328.5334	0.0000	1.0000
F81I	39	-2625.0419	5331.4460	0.0000	1.0000
F81IG	40	-2624.2409	5332.0201	0.0000	1.0000
JC69G	36	-2634.9553	5344.7720	0.0000	1.0000
JC69I	36	-2635.5698	5346.0010	0.0000	1.0000
JC69IG	37	-2634.7640	5346.5516	0.0000	1.0000
F81	38	-2649.5258	5378.2420	0.0000	1.0000
JC69	35	-2658.7796	5390.2630	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-2569.3809	5226.7617	0.7243	0.7243
GTRG	44	-2570.8231	5229.6462	0.1712	0.8955
GTRIG	45	-2570.3355	5230.6709	0.1026	0.9981
HKYI	40	-2579.6061	5239.2123	0.0014	0.9995
HKYG	40	-2581.1124	5242.2248	0.0003	0.9998
HKYIG	41	-2580.6973	5243.3945	0.0002	1.0000
SYMG	41	-2587.5887	5257.1775	0.0000	1.0000
SYMIG	42	-2587.2116	5258.4233	0.0000	1.0000
SYMI	41	-2588.4561	5258.9122	0.0000	1.0000
K2PG	37	-2593.5240	5261.0480	0.0000	1.0000
K2PIG	38	-2593.1476	5262.2952	0.0000	1.0000
K2PI	37	-2594.4173	5262.8346	0.0000	1.0000
GTR	43	-2599.4859	5284.9719	0.0000	1.0000
HKY	39	-2608.8645	5295.7291	0.0000	1.0000
SYM	40	-2614.3071	5308.6141	0.0000	1.0000
K2P	36	-2620.2190	5312.4380	0.0000	1.0000
F81G	39	-2623.5857	5325.1714	0.0000	1.0000
F81I	39	-2625.0419	5328.0839	0.0000	1.0000
F81IG	40	-2624.2409	5328.4818	0.0000	1.0000
JC69G	36	-2634.9553	5341.9106	0.0000	1.0000
JC69I	36	-2635.5698	5343.1395	0.0000	1.0000
JC69IG	37	-2634.7640	5343.5279	0.0000	1.0000
F81	38	-2649.5258	5375.0515	0.0000	1.0000
JC69	35	-2658.7796	5387.5591	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-2579.6061	5434.2216	0.7640	0.7640
HKYG	40	-2581.1124	5437.2341	0.1694	0.9334
GTRI	44	-2569.3809	5441.2719	0.0225	0.9559
K2PG	37	-2593.5240	5441.4316	0.0208	0.9767
K2PI	37	-2594.4173	5443.2182	0.0085	0.9852
HKYIG	41	-2580.6973	5443.2790	0.0082	0.9934
GTRG	44	-2570.8231	5444.1564	0.0053	0.9987
K2PIG	38	-2593.1476	5447.5540	0.0010	0.9997
GTRIG	45	-2570.3355	5450.0563	0.0003	1.0000
SYMG	41	-2587.5887	5457.0620	0.0000	1.0000
SYMI	41	-2588.4561	5458.7967	0.0000	1.0000
SYMIG	42	-2587.2116	5463.1830	0.0000	1.0000
HKY	39	-2608.8645	5485.8631	0.0000	1.0000
K2P	36	-2620.2190	5487.9464	0.0000	1.0000
GTR	43	-2599.4859	5494.6068	0.0000	1.0000
SYM	40	-2614.3071	5503.6234	0.0000	1.0000
F81G	39	-2623.5857	5515.3054	0.0000	1.0000
JC69G	36	-2634.9553	5517.4189	0.0000	1.0000
F81I	39	-2625.0419	5518.2180	0.0000	1.0000
JC69I	36	-2635.5698	5518.6479	0.0000	1.0000
F81IG	40	-2624.2409	5523.4910	0.0000	1.0000
JC69IG	37	-2634.7640	5523.9115	0.0000	1.0000
JC69	35	-2658.7796	5558.1923	0.0000	1.0000
F81	38	-2649.5258	5560.3103	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/chr7_5015.phylip = 1 - 968;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_5015.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/chr7_5015.phylip = 1 - 968;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_5015.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/chr7_5015.phylip = 1 - 968;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_5015.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

