
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:19 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_32389.phylip" (19 taxa, 470 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PIG


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	-1826.9036	3751.1248	0.8444	0.8444
HKYIG	41	-1832.2468	3754.5403	0.1531	0.9975
K2PIG	38	-1840.6962	3764.2695	0.0012	0.9987
GTRI	44	-1834.5605	3766.4387	0.0004	0.9991
SYMG	41	-1838.7001	3767.4470	0.0002	0.9993
HKYI	40	-1839.9228	3767.4912	0.0002	0.9995
SYMIG	42	-1837.7291	3767.9173	0.0002	0.9997
HKYG	40	-1840.5156	3768.6769	0.0001	0.9999
GTRIG	45	-1834.4856	3768.7353	0.0001	1.0000
K2PI	37	-1847.5037	3775.5166	0.0000	1.0000
K2PG	37	-1848.1137	3776.7367	0.0000	1.0000
SYMI	41	-1844.9735	3779.9937	0.0000	1.0000
GTR	43	-1861.0528	3816.9882	0.0000	1.0000
HKY	39	-1867.2652	3819.7862	0.0000	1.0000
K2P	36	-1875.8421	3829.8366	0.0000	1.0000
SYM	40	-1872.5962	3832.8381	0.0000	1.0000
JC69IG	37	-1883.2885	3847.0863	0.0000	1.0000
F81I	39	-1881.7354	3848.7266	0.0000	1.0000
F81G	39	-1882.0989	3849.4536	0.0000	1.0000
F81IG	40	-1881.5026	3850.6510	0.0000	1.0000
JC69I	36	-1887.5833	3853.3190	0.0000	1.0000
JC69G	36	-1888.0184	3854.1892	0.0000	1.0000
F81	38	-1907.8708	3898.6186	0.0000	1.0000
JC69	35	-1914.3682	3904.5429	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1826.9036	3741.8072	0.9111	0.9111
HKYIG	41	-1832.2468	3746.4935	0.0875	0.9986
GTRI	44	-1834.5605	3757.1211	0.0004	0.9990
K2PIG	38	-1840.6962	3757.3924	0.0004	0.9994
GTRIG	45	-1834.4856	3758.9712	0.0002	0.9996
SYMG	41	-1838.7001	3759.4002	0.0001	0.9997
SYMIG	42	-1837.7291	3759.4583	0.0001	0.9998
HKYI	40	-1839.9228	3759.8455	0.0001	0.9999
HKYG	40	-1840.5156	3761.0312	0.0001	1.0000
K2PI	37	-1847.5037	3769.0073	0.0000	1.0000
K2PG	37	-1848.1137	3770.2275	0.0000	1.0000
SYMI	41	-1844.9735	3771.9470	0.0000	1.0000
GTR	43	-1861.0528	3808.1055	0.0000	1.0000
HKY	39	-1867.2652	3812.5303	0.0000	1.0000
K2P	36	-1875.8421	3823.6842	0.0000	1.0000
SYM	40	-1872.5962	3825.1925	0.0000	1.0000
JC69IG	37	-1883.2885	3840.5770	0.0000	1.0000
F81I	39	-1881.7354	3841.4708	0.0000	1.0000
F81G	39	-1882.0989	3842.1978	0.0000	1.0000
F81IG	40	-1881.5026	3843.0053	0.0000	1.0000
JC69I	36	-1887.5833	3847.1666	0.0000	1.0000
JC69G	36	-1888.0184	3848.0368	0.0000	1.0000
F81	38	-1907.8708	3891.7415	0.0000	1.0000
JC69	35	-1914.3682	3898.7365	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PIG	38	-1840.6962	3915.1963	0.6610	0.6610
HKYIG	41	-1832.2468	3916.7556	0.3031	0.9641
K2PI	37	-1847.5037	3922.6584	0.0158	0.9799
K2PG	37	-1848.1137	3923.8786	0.0086	0.9885
GTRG	44	-1826.9036	3924.5274	0.0062	0.9947
HKYI	40	-1839.9228	3925.9548	0.0030	0.9978
HKYG	40	-1840.5156	3927.1405	0.0017	0.9995
SYMG	41	-1838.7001	3929.6623	0.0005	0.9999
SYMIG	42	-1837.7291	3933.8731	0.0001	1.0000
GTRI	44	-1834.5605	3939.8413	0.0000	1.0000
SYMI	41	-1844.9735	3942.2091	0.0000	1.0000
GTRIG	45	-1834.4856	3945.8442	0.0000	1.0000
K2P	36	-1875.8421	3973.1826	0.0000	1.0000
HKY	39	-1867.2652	3974.4869	0.0000	1.0000
GTR	43	-1861.0528	3986.6730	0.0000	1.0000
SYM	40	-1872.5962	3991.3018	0.0000	1.0000
JC69IG	37	-1883.2885	3994.2281	0.0000	1.0000
JC69I	36	-1887.5833	3996.6649	0.0000	1.0000
JC69G	36	-1888.0184	3997.5352	0.0000	1.0000
F81I	39	-1881.7354	4003.4274	0.0000	1.0000
F81G	39	-1882.0989	4004.1543	0.0000	1.0000
F81IG	40	-1881.5026	4009.1146	0.0000	1.0000
JC69	35	-1914.3682	4044.0821	0.0000	1.0000
F81	38	-1907.8708	4049.5454	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/chr1_32389.phylip = 1 - 470;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32389.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/chr1_32389.phylip = 1 - 470;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32389.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 (K2PIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32389.phylip = 1 - 470;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32389.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

