
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:13 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/chrZ_467.phylip" (19 taxa, 290 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
Minimum BIC  model: K2PG


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
HKYG	40	-748.4324	1590.0374	0.3522	0.3522
HKYI	40	-748.9663	1591.1054	0.2065	0.5587
HKYIG	41	-748.3656	1592.6183	0.0969	0.6556
K2PG	37	-753.9068	1592.9724	0.0812	0.7368
GTRG	44	-744.5083	1593.1799	0.0732	0.8100
K2PI	37	-754.3725	1593.9038	0.0510	0.8610
GTRI	44	-745.1247	1594.4126	0.0395	0.9005
HKY	39	-752.1747	1594.8294	0.0321	0.9326
K2PIG	38	-753.8227	1595.4542	0.0235	0.9560
GTRIG	45	-744.4724	1595.9120	0.0187	0.9747
GTR	43	-747.7661	1596.9144	0.0113	0.9860
K2P	36	-758.0675	1598.6647	0.0047	0.9907
SYMG	41	-751.8812	1599.6495	0.0029	0.9936
SYMI	41	-752.4038	1600.6947	0.0017	0.9953
F81G	39	-755.3529	1601.1859	0.0013	0.9967
F81I	39	-755.8241	1602.1281	0.0008	0.9975
SYMIG	42	-751.8263	1602.2760	0.0008	0.9983
JC69G	36	-760.3544	1603.2384	0.0005	0.9987
F81IG	40	-755.2934	1603.7594	0.0004	0.9991
JC69I	36	-760.7843	1604.0982	0.0003	0.9994
SYM	40	-755.4781	1604.1289	0.0003	0.9997
JC69IG	37	-760.2807	1605.7201	0.0001	0.9999
F81	38	-759.2221	1606.2530	0.0001	1.0000
JC69	35	-764.5423	1609.0058	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-748.4324	1576.8647	0.2423	0.2423
GTRG	44	-744.5083	1577.0167	0.2246	0.4670
HKYI	40	-748.9663	1577.9327	0.1421	0.6090
GTRI	44	-745.1247	1578.2494	0.1213	0.7303
HKYIG	41	-748.3656	1578.7312	0.0953	0.8256
GTRIG	45	-744.4724	1578.9448	0.0857	0.9113
GTR	43	-747.7661	1581.5322	0.0235	0.9348
K2PG	37	-753.9068	1581.8137	0.0204	0.9552
HKY	39	-752.1747	1582.3494	0.0156	0.9708
K2PI	37	-754.3725	1582.7450	0.0128	0.9836
K2PIG	38	-753.8227	1583.6455	0.0082	0.9918
SYMG	41	-751.8812	1585.7624	0.0028	0.9946
SYMI	41	-752.4038	1586.8076	0.0017	0.9963
SYMIG	42	-751.8263	1587.6526	0.0011	0.9974
K2P	36	-758.0675	1588.1350	0.0009	0.9983
F81G	39	-755.3529	1588.7059	0.0007	0.9989
F81I	39	-755.8241	1589.6481	0.0004	0.9993
F81IG	40	-755.2934	1590.5867	0.0003	0.9996
SYM	40	-755.4781	1590.9562	0.0002	0.9998
JC69G	36	-760.3544	1592.7087	0.0001	0.9999
JC69I	36	-760.7843	1593.5685	0.0001	0.9999
F81	38	-759.2221	1594.4443	0.0000	1.0000
JC69IG	37	-760.2807	1594.5613	0.0000	1.0000
JC69	35	-764.5423	1599.0846	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-753.9068	1717.5993	0.4736	0.4736
K2PI	37	-754.3725	1718.5306	0.2973	0.7709
K2P	36	-758.0675	1720.2508	0.1258	0.8967
K2PIG	38	-753.8227	1723.1010	0.0303	0.9269
HKYG	40	-748.4324	1723.6600	0.0229	0.9498
HKYI	40	-748.9663	1724.7279	0.0134	0.9632
JC69G	36	-760.3544	1724.8245	0.0128	0.9760
HKY	39	-752.1747	1725.4747	0.0092	0.9852
JC69I	36	-760.7843	1725.6843	0.0083	0.9935
JC69	35	-764.5423	1727.5304	0.0033	0.9968
HKYIG	41	-748.3656	1729.1963	0.0014	0.9983
JC69IG	37	-760.2807	1730.3469	0.0008	0.9991
F81G	39	-755.3529	1731.8312	0.0004	0.9995
F81I	39	-755.8241	1732.7735	0.0002	0.9997
F81	38	-759.2221	1733.8997	0.0001	0.9999
SYMG	41	-751.8812	1736.2275	0.0000	0.9999
SYMI	41	-752.4038	1737.2727	0.0000	0.9999
F81IG	40	-755.2934	1737.3820	0.0000	0.9999
SYM	40	-755.4781	1737.7514	0.0000	1.0000
GTRG	44	-744.5083	1738.4914	0.0000	1.0000
GTR	43	-747.7661	1739.3371	0.0000	1.0000
GTRI	44	-745.1247	1739.7241	0.0000	1.0000
SYMIG	42	-751.8263	1741.7876	0.0000	1.0000
GTRIG	45	-744.4724	1744.0895	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_467.phylip = 1 - 290;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_467.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_467.phylip = 1 - 290;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_467.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;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_467.phylip = 1 - 290;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_467.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

