
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
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/chr3_17712.phylip" (19 taxa, 897 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: HKYG


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	-3713.8679	7520.3836	0.5995	0.5995
GTRIG	45	-3713.1635	7521.1918	0.4002	0.9997
HKYG	40	-3726.2033	7536.2383	0.0002	0.9999
HKYIG	41	-3725.8990	7537.8261	0.0001	1.0000
GTRI	44	-3732.5012	7557.6504	0.0000	1.0000
HKYI	40	-3742.2413	7568.3144	0.0000	1.0000
SYMG	41	-3764.6400	7615.3081	0.0000	1.0000
SYMIG	42	-3764.2247	7616.6790	0.0000	1.0000
K2PG	37	-3770.1766	7617.6268	0.0000	1.0000
K2PIG	38	-3769.7554	7618.9654	0.0000	1.0000
SYMI	41	-3776.7017	7639.4315	0.0000	1.0000
K2PI	37	-3782.4996	7642.2728	0.0000	1.0000
GTR	43	-3799.1493	7688.7347	0.0000	1.0000
HKY	39	-3808.4705	7698.5817	0.0000	1.0000
SYM	40	-3850.5323	7784.8964	0.0000	1.0000
F81G	39	-3851.6340	7784.9086	0.0000	1.0000
F81IG	40	-3851.2981	7786.4280	0.0000	1.0000
K2P	36	-3857.5595	7790.2168	0.0000	1.0000
F81I	39	-3864.0642	7809.7689	0.0000	1.0000
JC69G	36	-3884.0898	7843.2772	0.0000	1.0000
JC69IG	37	-3883.7039	7844.6814	0.0000	1.0000
JC69I	36	-3895.3328	7865.7633	0.0000	1.0000
F81	38	-3924.8306	7929.1156	0.0000	1.0000
JC69	35	-3960.0796	7993.0860	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3713.8679	7515.7357	0.5733	0.5733
GTRIG	45	-3713.1635	7516.3270	0.4265	0.9998
HKYG	40	-3726.2033	7532.4066	0.0001	0.9999
HKYIG	41	-3725.8990	7533.7980	0.0001	1.0000
GTRI	44	-3732.5012	7553.0025	0.0000	1.0000
HKYI	40	-3742.2413	7564.4826	0.0000	1.0000
SYMG	41	-3764.6400	7611.2800	0.0000	1.0000
SYMIG	42	-3764.2247	7612.4495	0.0000	1.0000
K2PG	37	-3770.1766	7614.3533	0.0000	1.0000
K2PIG	38	-3769.7554	7615.5109	0.0000	1.0000
SYMI	41	-3776.7017	7635.4034	0.0000	1.0000
K2PI	37	-3782.4996	7638.9992	0.0000	1.0000
GTR	43	-3799.1493	7684.2986	0.0000	1.0000
HKY	39	-3808.4705	7694.9411	0.0000	1.0000
SYM	40	-3850.5323	7781.0646	0.0000	1.0000
F81G	39	-3851.6340	7781.2680	0.0000	1.0000
F81IG	40	-3851.2981	7782.5962	0.0000	1.0000
K2P	36	-3857.5595	7787.1191	0.0000	1.0000
F81I	39	-3864.0642	7806.1283	0.0000	1.0000
JC69G	36	-3884.0898	7840.1795	0.0000	1.0000
JC69IG	37	-3883.7039	7841.4078	0.0000	1.0000
JC69I	36	-3895.3328	7862.6656	0.0000	1.0000
F81	38	-3924.8306	7925.6611	0.0000	1.0000
JC69	35	-3960.0796	7990.1592	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3726.2033	7724.3688	0.7422	0.7422
GTRG	44	-3713.8679	7726.8942	0.2100	0.9522
HKYIG	41	-3725.8990	7730.5593	0.0336	0.9858
GTRIG	45	-3713.1635	7732.2845	0.0142	1.0000
HKYI	40	-3742.2413	7756.4448	0.0000	1.0000
GTRI	44	-3732.5012	7764.1610	0.0000	1.0000
K2PG	37	-3770.1766	7791.9183	0.0000	1.0000
K2PIG	38	-3769.7554	7797.8750	0.0000	1.0000
SYMG	41	-3764.6400	7808.0413	0.0000	1.0000
SYMIG	42	-3764.2247	7814.0098	0.0000	1.0000
K2PI	37	-3782.4996	7816.5642	0.0000	1.0000
SYMI	41	-3776.7017	7832.1647	0.0000	1.0000
HKY	39	-3808.4705	7882.1043	0.0000	1.0000
GTR	43	-3799.1493	7890.6580	0.0000	1.0000
K2P	36	-3857.5595	7959.8851	0.0000	1.0000
F81G	39	-3851.6340	7968.4312	0.0000	1.0000
SYM	40	-3850.5323	7973.0268	0.0000	1.0000
F81IG	40	-3851.2981	7974.5584	0.0000	1.0000
F81I	39	-3864.0642	7993.2915	0.0000	1.0000
JC69G	36	-3884.0898	8012.9455	0.0000	1.0000
JC69IG	37	-3883.7039	8018.9728	0.0000	1.0000
JC69I	36	-3895.3328	8035.4316	0.0000	1.0000
F81	38	-3924.8306	8108.0252	0.0000	1.0000
JC69	35	-3960.0796	8158.1261	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/chr3_17712.phylip = 1 - 897;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17712.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/chr3_17712.phylip = 1 - 897;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17712.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17712.phylip = 1 - 897;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17712.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;


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End of Output

