
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:54 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/chr2_21278.phylip" (19 taxa, 705 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: SYMG


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	-2399.2025	4892.4051	0.7069	0.7069
GTRIG	45	-2398.9895	4894.2612	0.2795	0.9864
GTRI	44	-2403.3114	4900.6229	0.0116	0.9980
SYMG	41	-2408.9945	4905.1835	0.0012	0.9992
SYMIG	42	-2408.4333	4906.3227	0.0007	0.9999
HKYG	40	-2412.8462	4910.6321	0.0001	0.9999
SYMI	41	-2412.3941	4911.9828	0.0000	1.0000
HKYIG	41	-2413.0538	4913.3022	0.0000	1.0000
HKYI	40	-2414.9778	4914.8953	0.0000	1.0000
K2PG	37	-2429.2922	4936.8002	0.0000	1.0000
K2PIG	38	-2428.6788	4937.8080	0.0000	1.0000
K2PI	37	-2432.0488	4942.3136	0.0000	1.0000
GTR	43	-2452.4929	4996.7105	0.0000	1.0000
F81G	39	-2460.5480	5003.7876	0.0000	1.0000
F81IG	40	-2459.9564	5004.8525	0.0000	1.0000
SYM	40	-2460.0323	5005.0044	0.0000	1.0000
F81I	39	-2463.0696	5008.8310	0.0000	1.0000
HKY	39	-2465.1299	5012.9515	0.0000	1.0000
K2P	36	-2481.0025	5037.9929	0.0000	1.0000
JC69G	36	-2482.2676	5040.5233	0.0000	1.0000
JC69IG	37	-2481.7934	5041.8027	0.0000	1.0000
JC69I	36	-2484.6576	5045.3033	0.0000	1.0000
F81	38	-2512.6220	5105.6945	0.0000	1.0000
JC69	35	-2531.8082	5137.3833	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2399.2025	4886.4051	0.6786	0.6786
GTRIG	45	-2398.9895	4887.9790	0.3089	0.9875
GTRI	44	-2403.3114	4894.6229	0.0111	0.9987
SYMG	41	-2408.9945	4899.9890	0.0008	0.9994
SYMIG	42	-2408.4333	4900.8665	0.0005	0.9999
HKYG	40	-2412.8462	4905.6924	0.0000	1.0000
SYMI	41	-2412.3941	4906.7882	0.0000	1.0000
HKYIG	41	-2413.0538	4908.1076	0.0000	1.0000
HKYI	40	-2414.9778	4909.9556	0.0000	1.0000
K2PG	37	-2429.2922	4932.5843	0.0000	1.0000
K2PIG	38	-2428.6788	4933.3575	0.0000	1.0000
K2PI	37	-2432.0488	4938.0977	0.0000	1.0000
GTR	43	-2452.4929	4990.9858	0.0000	1.0000
F81G	39	-2460.5480	4999.0959	0.0000	1.0000
F81IG	40	-2459.9564	4999.9127	0.0000	1.0000
SYM	40	-2460.0323	5000.0646	0.0000	1.0000
F81I	39	-2463.0696	5004.1393	0.0000	1.0000
HKY	39	-2465.1299	5008.2597	0.0000	1.0000
K2P	36	-2481.0025	5034.0049	0.0000	1.0000
JC69G	36	-2482.2676	5036.5352	0.0000	1.0000
JC69IG	37	-2481.7934	5037.5868	0.0000	1.0000
JC69I	36	-2484.6576	5041.3152	0.0000	1.0000
F81	38	-2512.6220	5101.2441	0.0000	1.0000
JC69	35	-2531.8082	5133.6165	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
SYMG	41	-2408.9945	5086.8751	0.3617	0.3617
GTRG	44	-2399.2025	5086.9658	0.3457	0.7074
HKYG	40	-2412.8462	5088.0203	0.2040	0.9115
HKYI	40	-2414.9778	5092.2835	0.0242	0.9357
SYMIG	42	-2408.4333	5092.3108	0.0239	0.9596
GTRIG	45	-2398.9895	5093.0979	0.0161	0.9757
SYMI	41	-2412.3941	5093.6743	0.0121	0.9878
HKYIG	41	-2413.0538	5094.9937	0.0062	0.9940
GTRI	44	-2403.3114	5095.1836	0.0057	0.9997
K2PG	37	-2429.2922	5101.2376	0.0003	1.0000
K2PIG	38	-2428.6788	5106.5690	0.0000	1.0000
K2PI	37	-2432.0488	5106.7510	0.0000	1.0000
F81G	39	-2460.5480	5176.8656	0.0000	1.0000
F81I	39	-2463.0696	5181.9090	0.0000	1.0000
F81IG	40	-2459.9564	5182.2407	0.0000	1.0000
SYM	40	-2460.0323	5182.3925	0.0000	1.0000
HKY	39	-2465.1299	5186.0295	0.0000	1.0000
GTR	43	-2452.4929	5186.9883	0.0000	1.0000
K2P	36	-2481.0025	5198.1000	0.0000	1.0000
JC69G	36	-2482.2676	5200.6304	0.0000	1.0000
JC69I	36	-2484.6576	5205.4104	0.0000	1.0000
JC69IG	37	-2481.7934	5206.2401	0.0000	1.0000
F81	38	-2512.6220	5274.4556	0.0000	1.0000
JC69	35	-2531.8082	5293.1534	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/chr2_21278.phylip = 1 - 705;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21278.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/chr2_21278.phylip = 1 - 705;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21278.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 (SYMG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21278.phylip = 1 - 705;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21278.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=Fixed(Equal);
END;


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End of Output

