
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:10 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/chr1_10281.phylip" (19 taxa, 461 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	-1874.4670	3836.7436	0.6091	0.6091
HKYIG	41	-1874.3695	3838.9586	0.2012	0.8103
GTRG	44	-1871.7310	3840.9813	0.0732	0.8835
K2PG	37	-1880.2074	3841.0625	0.0703	0.9538
K2PIG	38	-1880.1100	3843.2438	0.0236	0.9774
GTRIG	45	-1872.4275	3844.8309	0.0107	0.9881
SYMG	41	-1877.6863	3845.5922	0.0073	0.9954
SYMIG	42	-1877.5991	3847.8392	0.0024	0.9977
HKYI	40	-1880.2890	3848.3876	0.0018	0.9995
GTRI	44	-1877.3388	3852.1968	0.0003	0.9998
K2PI	37	-1886.3576	3853.3629	0.0001	1.0000
SYMI	41	-1882.8759	3855.9713	0.0000	1.0000
HKY	39	-1924.9798	3935.3706	0.0000	1.0000
K2P	36	-1929.1360	3936.5549	0.0000	1.0000
GTR	43	-1923.1907	3941.4557	0.0000	1.0000
SYM	40	-1929.2349	3946.2793	0.0000	1.0000
F81G	39	-1932.8947	3951.2003	0.0000	1.0000
JC69IG	37	-1936.9217	3954.4913	0.0000	1.0000
JC69G	36	-1939.8730	3958.0290	0.0000	1.0000
F81IG	40	-1935.8857	3959.5808	0.0000	1.0000
JC69I	36	-1942.1993	3962.6816	0.0000	1.0000
F81I	39	-1941.2157	3967.8423	0.0000	1.0000
F81	38	-1980.0571	4043.1379	0.0000	1.0000
JC69	35	-1988.3466	4052.6226	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1874.4670	3828.9341	0.5390	0.5390
HKYIG	41	-1874.3695	3830.7390	0.2186	0.7575
GTRG	44	-1871.7310	3831.4621	0.1523	0.9098
K2PG	37	-1880.2074	3834.4147	0.0348	0.9446
GTRIG	45	-1872.4275	3834.8550	0.0279	0.9725
K2PIG	38	-1880.1100	3836.2201	0.0141	0.9866
SYMG	41	-1877.6863	3837.3726	0.0079	0.9945
SYMIG	42	-1877.5991	3839.1981	0.0032	0.9977
HKYI	40	-1880.2890	3840.5780	0.0016	0.9993
GTRI	44	-1877.3388	3842.6776	0.0006	0.9999
K2PI	37	-1886.3576	3846.7151	0.0001	1.0000
SYMI	41	-1882.8759	3847.7518	0.0000	1.0000
HKY	39	-1924.9798	3927.9597	0.0000	1.0000
K2P	36	-1929.1360	3930.2719	0.0000	1.0000
GTR	43	-1923.1907	3932.3814	0.0000	1.0000
SYM	40	-1929.2349	3938.4698	0.0000	1.0000
F81G	39	-1932.8947	3943.7894	0.0000	1.0000
JC69IG	37	-1936.9217	3947.8435	0.0000	1.0000
JC69G	36	-1939.8730	3951.7460	0.0000	1.0000
F81IG	40	-1935.8857	3951.7713	0.0000	1.0000
JC69I	36	-1942.1993	3956.3986	0.0000	1.0000
F81I	39	-1941.2157	3960.4314	0.0000	1.0000
F81	38	-1980.0571	4036.1142	0.0000	1.0000
JC69	35	-1988.3466	4046.6932	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1880.2074	3987.3504	0.9202	0.9202
K2PIG	38	-1880.1100	3993.2892	0.0472	0.9675
HKYG	40	-1874.4670	3994.2700	0.0289	0.9964
K2PI	37	-1886.3576	3999.6508	0.0020	0.9984
HKYIG	41	-1874.3695	4000.2083	0.0015	0.9999
HKYI	40	-1880.2890	4005.9140	0.0001	0.9999
SYMG	41	-1877.6863	4006.8419	0.0001	1.0000
SYMIG	42	-1877.5991	4012.8008	0.0000	1.0000
GTRG	44	-1871.7310	4013.3316	0.0000	1.0000
SYMI	41	-1882.8759	4017.2211	0.0000	1.0000
GTRIG	45	-1872.4275	4020.8579	0.0000	1.0000
GTRI	44	-1877.3388	4024.5471	0.0000	1.0000
K2P	36	-1929.1360	4079.0742	0.0000	1.0000
HKY	39	-1924.9798	4089.1622	0.0000	1.0000
JC69G	36	-1939.8730	4100.5483	0.0000	1.0000
JC69IG	37	-1936.9217	4100.7792	0.0000	1.0000
SYM	40	-1929.2349	4103.8057	0.0000	1.0000
F81G	39	-1932.8947	4104.9919	0.0000	1.0000
JC69I	36	-1942.1993	4105.2009	0.0000	1.0000
GTR	43	-1923.1907	4110.1175	0.0000	1.0000
F81IG	40	-1935.8857	4117.1072	0.0000	1.0000
F81I	39	-1941.2157	4121.6339	0.0000	1.0000
JC69	35	-1988.3466	4191.3621	0.0000	1.0000
F81	38	-1980.0571	4193.1833	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/chr1_10281.phylip = 1 - 461;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_10281.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/chr1_10281.phylip = 1 - 461;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_10281.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/chr1_10281.phylip = 1 - 461;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_10281.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

