
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:02 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_17806.phylip" (19 taxa, 670 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	-3517.6626	7129.6612	0.5252	0.5252
GTRIG	45	-3516.8611	7130.3569	0.3709	0.8960
GTRI	44	-3519.9796	7134.2951	0.0518	0.9478
HKYG	40	-3525.0266	7135.2678	0.0318	0.9796
HKYIG	41	-3524.5064	7136.4969	0.0172	0.9968
HKYI	40	-3527.3358	7139.8862	0.0032	1.0000
SYMG	41	-3536.4642	7160.4126	0.0000	1.0000
SYMIG	42	-3535.7184	7161.1975	0.0000	1.0000
K2PG	37	-3541.4210	7161.2913	0.0000	1.0000
K2PIG	38	-3540.8864	7162.4700	0.0000	1.0000
SYMI	41	-3538.4961	7164.4762	0.0000	1.0000
K2PI	37	-3543.7919	7166.0331	0.0000	1.0000
GTR	43	-3580.9877	7254.0201	0.0000	1.0000
HKY	39	-3590.3093	7263.5710	0.0000	1.0000
F81IG	40	-3598.3743	7281.9632	0.0000	1.0000
F81G	39	-3600.0528	7283.0580	0.0000	1.0000
SYM	40	-3599.7262	7284.6670	0.0000	1.0000
F81I	39	-3601.1174	7285.1872	0.0000	1.0000
K2P	36	-3606.6768	7289.5622	0.0000	1.0000
JC69IG	37	-3609.2727	7296.9947	0.0000	1.0000
JC69G	36	-3610.7398	7297.6882	0.0000	1.0000
JC69I	36	-3612.7666	7301.7418	0.0000	1.0000
F81	38	-3660.7267	7402.1507	0.0000	1.0000
JC69	35	-3672.3907	7418.7561	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3517.6626	7123.3252	0.5056	0.5056
GTRIG	45	-3516.8611	7123.7223	0.4145	0.9201
GTRI	44	-3519.9796	7127.9591	0.0498	0.9699
HKYG	40	-3525.0266	7130.0532	0.0175	0.9874
HKYIG	41	-3524.5064	7131.0128	0.0108	0.9983
HKYI	40	-3527.3358	7134.6715	0.0017	1.0000
SYMG	41	-3536.4642	7154.9285	0.0000	1.0000
SYMIG	42	-3535.7184	7155.4367	0.0000	1.0000
K2PG	37	-3541.4210	7156.8420	0.0000	1.0000
K2PIG	38	-3540.8864	7157.7727	0.0000	1.0000
SYMI	41	-3538.4961	7158.9921	0.0000	1.0000
K2PI	37	-3543.7919	7161.5837	0.0000	1.0000
GTR	43	-3580.9877	7247.9754	0.0000	1.0000
HKY	39	-3590.3093	7258.6187	0.0000	1.0000
F81IG	40	-3598.3743	7276.7485	0.0000	1.0000
F81G	39	-3600.0528	7278.1056	0.0000	1.0000
SYM	40	-3599.7262	7279.4524	0.0000	1.0000
F81I	39	-3601.1174	7280.2348	0.0000	1.0000
K2P	36	-3606.6768	7285.3536	0.0000	1.0000
JC69IG	37	-3609.2727	7292.5453	0.0000	1.0000
JC69G	36	-3610.7398	7293.4796	0.0000	1.0000
JC69I	36	-3612.7666	7297.5333	0.0000	1.0000
F81	38	-3660.7267	7397.4534	0.0000	1.0000
JC69	35	-3672.3907	7414.7813	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3525.0266	7310.3443	0.8547	0.8547
HKYI	40	-3527.3358	7314.9626	0.0849	0.9396
HKYIG	41	-3524.5064	7315.8112	0.0555	0.9951
GTRG	44	-3517.6626	7321.6454	0.0030	0.9981
K2PG	37	-3541.4210	7323.6112	0.0011	0.9993
GTRI	44	-3519.9796	7326.2793	0.0003	0.9996
GTRIG	45	-3516.8611	7326.5498	0.0003	0.9998
K2PI	37	-3543.7919	7328.3530	0.0001	0.9999
K2PIG	38	-3540.8864	7329.0493	0.0001	1.0000
SYMG	41	-3536.4642	7339.7269	0.0000	1.0000
SYMI	41	-3538.4961	7343.7905	0.0000	1.0000
SYMIG	42	-3535.7184	7344.7424	0.0000	1.0000
HKY	39	-3590.3093	7434.4025	0.0000	1.0000
GTR	43	-3580.9877	7441.7883	0.0000	1.0000
K2P	36	-3606.6768	7447.6156	0.0000	1.0000
F81G	39	-3600.0528	7453.8895	0.0000	1.0000
JC69G	36	-3610.7398	7455.7416	0.0000	1.0000
F81I	39	-3601.1174	7456.0187	0.0000	1.0000
F81IG	40	-3598.3743	7457.0396	0.0000	1.0000
JC69IG	37	-3609.2727	7459.3146	0.0000	1.0000
SYM	40	-3599.7262	7459.7435	0.0000	1.0000
JC69I	36	-3612.7666	7459.7953	0.0000	1.0000
F81	38	-3660.7267	7568.7300	0.0000	1.0000
JC69	35	-3672.3907	7572.5360	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_17806.phylip = 1 - 670;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17806.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_17806.phylip = 1 - 670;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17806.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_17806.phylip = 1 - 670;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17806.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

