
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:25 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/chr9_1157.phylip" (19 taxa, 376 characters)

Minimum AIC  model: HKYIG
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	-1983.7880	4057.3671	0.3201	0.3201
HKYIG	41	-1982.6828	4057.6769	0.2742	0.5943
HKYI	40	-1984.3902	4058.5714	0.1753	0.7696
K2PG	37	-1988.9962	4060.3119	0.0734	0.8430
K2PIG	38	-1987.9491	4060.6934	0.0607	0.9037
K2PI	37	-1989.4919	4061.3033	0.0447	0.9484
SYMG	41	-1985.4629	4063.2372	0.0170	0.9654
SYMIG	42	-1984.6890	4064.2249	0.0104	0.9758
GTRG	44	-1982.2174	4064.3985	0.0095	0.9853
SYMI	41	-1986.5224	4065.3562	0.0059	0.9912
GTRIG	45	-1981.4142	4065.3738	0.0058	0.9971
GTRI	44	-1983.4001	4066.7640	0.0029	1.0000
HKY	39	-2001.3032	4089.8921	0.0000	1.0000
SYM	40	-2000.2783	4090.3475	0.0000	1.0000
K2P	36	-2005.4315	4090.7214	0.0000	1.0000
GTR	43	-1999.1594	4095.7164	0.0000	1.0000
F81I	39	-2031.7358	4150.7573	0.0000	1.0000
F81G	39	-2031.7359	4150.7576	0.0000	1.0000
JC69G	36	-2035.5084	4150.8752	0.0000	1.0000
F81IG	40	-2030.5693	4150.9297	0.0000	1.0000
JC69I	36	-2035.5706	4150.9996	0.0000	1.0000
JC69IG	37	-2034.4183	4151.1560	0.0000	1.0000
JC69	35	-2050.1997	4177.8112	0.0000	1.0000
F81	38	-2046.9496	4178.6945	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-1982.6828	4047.3655	0.3381	0.3381
HKYG	40	-1983.7880	4047.5761	0.3043	0.6424
HKYI	40	-1984.3902	4048.7804	0.1667	0.8091
K2PIG	38	-1987.9491	4051.8982	0.0351	0.8442
K2PG	37	-1988.9962	4051.9924	0.0334	0.8776
GTRG	44	-1982.2174	4052.4348	0.0268	0.9044
GTRIG	45	-1981.4142	4052.8284	0.0220	0.9264
SYMG	41	-1985.4629	4052.9258	0.0210	0.9474
K2PI	37	-1989.4919	4052.9838	0.0204	0.9678
SYMIG	42	-1984.6890	4053.3780	0.0167	0.9845
GTRI	44	-1983.4001	4054.8002	0.0082	0.9927
SYMI	41	-1986.5224	4055.0448	0.0073	1.0000
SYM	40	-2000.2783	4080.5565	0.0000	1.0000
HKY	39	-2001.3032	4080.6064	0.0000	1.0000
K2P	36	-2005.4315	4082.8630	0.0000	1.0000
GTR	43	-1999.1594	4084.3188	0.0000	1.0000
F81IG	40	-2030.5693	4141.1387	0.0000	1.0000
F81I	39	-2031.7358	4141.4716	0.0000	1.0000
F81G	39	-2031.7359	4141.4719	0.0000	1.0000
JC69IG	37	-2034.4183	4142.8365	0.0000	1.0000
JC69G	36	-2035.5084	4143.0168	0.0000	1.0000
JC69I	36	-2035.5706	4143.1412	0.0000	1.0000
F81	38	-2046.9496	4169.8992	0.0000	1.0000
JC69	35	-2050.1997	4170.3994	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1988.9962	4197.3872	0.5558	0.5558
K2PI	37	-1989.4919	4198.3786	0.3386	0.8944
K2PIG	38	-1987.9491	4201.2225	0.0817	0.9761
HKYG	40	-1983.7880	4204.7596	0.0139	0.9900
HKYI	40	-1984.3902	4205.9639	0.0076	0.9976
HKYIG	41	-1982.6828	4208.4787	0.0022	0.9998
SYMG	41	-1985.4629	4214.0390	0.0001	0.9999
SYMI	41	-1986.5224	4216.1580	0.0000	1.0000
SYMIG	42	-1984.6890	4218.4208	0.0000	1.0000
K2P	36	-2005.4315	4224.3282	0.0000	1.0000
GTRG	44	-1982.2174	4225.3367	0.0000	1.0000
GTRI	44	-1983.4001	4227.7021	0.0000	1.0000
GTRIG	45	-1981.4142	4229.6599	0.0000	1.0000
HKY	39	-2001.3032	4233.8603	0.0000	1.0000
SYM	40	-2000.2783	4237.7401	0.0000	1.0000
GTR	43	-1999.1594	4253.2912	0.0000	1.0000
JC69G	36	-2035.5084	4284.4820	0.0000	1.0000
JC69I	36	-2035.5706	4284.6064	0.0000	1.0000
JC69IG	37	-2034.4183	4288.2313	0.0000	1.0000
F81I	39	-2031.7358	4294.7256	0.0000	1.0000
F81G	39	-2031.7359	4294.7259	0.0000	1.0000
F81IG	40	-2030.5693	4298.3222	0.0000	1.0000
JC69	35	-2050.1997	4307.9351	0.0000	1.0000
F81	38	-2046.9496	4319.2236	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/chr9_1157.phylip = 1 - 376;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_1157.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_1157.phylip = 1 - 376;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_1157.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/chr9_1157.phylip = 1 - 376;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_1157.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

