
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:59 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/chr5_9123.phylip" (19 taxa, 1044 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: HKYIG


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
GTRIG	45	-3669.7436	7433.6354	0.8669	0.8669
GTRG	44	-3673.2692	7438.5023	0.0761	0.9430
HKYIG	41	-3676.8941	7439.2253	0.0530	0.9960
HKYG	40	-3680.5606	7444.3914	0.0040	1.0000
GTRI	44	-3684.8016	7461.5671	0.0000	1.0000
HKYI	40	-3694.0948	7471.4598	0.0000	1.0000
F81IG	40	-3713.0345	7509.3391	0.0000	1.0000
F81G	39	-3716.1748	7513.4572	0.0000	1.0000
SYMIG	42	-3717.2415	7522.0914	0.0000	1.0000
SYMG	41	-3720.6374	7526.7119	0.0000	1.0000
F81I	39	-3726.7621	7534.6318	0.0000	1.0000
K2PIG	38	-3735.6247	7550.1987	0.0000	1.0000
SYMI	41	-3733.7237	7552.8846	0.0000	1.0000
K2PG	37	-3739.4152	7555.6256	0.0000	1.0000
K2PI	37	-3753.6305	7584.0562	0.0000	1.0000
JC69IG	37	-3767.1408	7611.0768	0.0000	1.0000
JC69G	36	-3770.1932	7615.0319	0.0000	1.0000
JC69I	36	-3780.9331	7636.5117	0.0000	1.0000
GTR	43	-3777.3082	7644.4005	0.0000	1.0000
HKY	39	-3793.9852	7669.0779	0.0000	1.0000
SYM	40	-3817.8355	7718.9412	0.0000	1.0000
F81	38	-3821.3155	7721.5803	0.0000	1.0000
K2P	36	-3847.9012	7770.4478	0.0000	1.0000
JC69	35	-3870.3531	7813.2062	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-3669.7436	7429.4871	0.8882	0.8882
GTRG	44	-3673.2692	7434.5383	0.0711	0.9593
HKYIG	41	-3676.8941	7435.7881	0.0380	0.9974
HKYG	40	-3680.5606	7441.1213	0.0026	1.0000
GTRI	44	-3684.8016	7457.6032	0.0000	1.0000
HKYI	40	-3694.0948	7468.1896	0.0000	1.0000
F81IG	40	-3713.0345	7506.0690	0.0000	1.0000
F81G	39	-3716.1748	7510.3496	0.0000	1.0000
SYMIG	42	-3717.2415	7518.4830	0.0000	1.0000
SYMG	41	-3720.6374	7523.2748	0.0000	1.0000
F81I	39	-3726.7621	7531.5242	0.0000	1.0000
K2PIG	38	-3735.6247	7547.2494	0.0000	1.0000
SYMI	41	-3733.7237	7549.4475	0.0000	1.0000
K2PG	37	-3739.4152	7552.8304	0.0000	1.0000
K2PI	37	-3753.6305	7581.2610	0.0000	1.0000
JC69IG	37	-3767.1408	7608.2816	0.0000	1.0000
JC69G	36	-3770.1932	7612.3864	0.0000	1.0000
JC69I	36	-3780.9331	7633.8662	0.0000	1.0000
GTR	43	-3777.3082	7640.6165	0.0000	1.0000
HKY	39	-3793.9852	7665.9704	0.0000	1.0000
SYM	40	-3817.8355	7715.6711	0.0000	1.0000
F81	38	-3821.3155	7718.6311	0.0000	1.0000
K2P	36	-3847.9012	7767.8023	0.0000	1.0000
JC69	35	-3870.3531	7810.7062	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYIG	41	-3676.8941	7638.7715	0.5470	0.5470
HKYG	40	-3680.5606	7639.1539	0.4518	0.9988
GTRIG	45	-3669.7436	7652.2738	0.0006	0.9994
GTRG	44	-3673.2692	7652.3742	0.0006	1.0000
HKYI	40	-3694.0948	7666.2222	0.0000	1.0000
GTRI	44	-3684.8016	7675.4390	0.0000	1.0000
F81G	39	-3716.1748	7703.4314	0.0000	1.0000
F81IG	40	-3713.0345	7704.1016	0.0000	1.0000
F81I	39	-3726.7621	7724.6060	0.0000	1.0000
SYMG	41	-3720.6374	7726.2582	0.0000	1.0000
SYMIG	42	-3717.2415	7726.4172	0.0000	1.0000
K2PIG	38	-3735.6247	7735.3804	0.0000	1.0000
K2PG	37	-3739.4152	7736.0105	0.0000	1.0000
SYMI	41	-3733.7237	7752.4309	0.0000	1.0000
K2PI	37	-3753.6305	7764.4411	0.0000	1.0000
JC69G	36	-3770.1932	7790.6157	0.0000	1.0000
JC69IG	37	-3767.1408	7791.4617	0.0000	1.0000
JC69I	36	-3780.9331	7812.0956	0.0000	1.0000
GTR	43	-3777.3082	7853.5015	0.0000	1.0000
HKY	39	-3793.9852	7859.0522	0.0000	1.0000
F81	38	-3821.3155	7906.7620	0.0000	1.0000
SYM	40	-3817.8355	7913.7037	0.0000	1.0000
K2P	36	-3847.9012	7946.0316	0.0000	1.0000
JC69	35	-3870.3531	7983.9847	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_9123.phylip = 1 - 1044;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_9123.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_9123.phylip = 1 - 1044;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_9123.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_9123.phylip = 1 - 1044;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_9123.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;


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End of Output

