
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:26 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/chr17_3028.phylip" (19 taxa, 681 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	-1738.4840	3571.1943	0.3907	0.3907
GTRI	44	-1738.8009	3571.8282	0.2846	0.6754
GTRIG	45	-1738.3553	3573.2302	0.1412	0.8165
HKYG	40	-1744.5629	3574.2507	0.0848	0.9013
HKYI	40	-1744.7770	3574.6790	0.0684	0.9697
HKYIG	41	-1744.4610	3576.3117	0.0302	1.0000
K2PG	37	-1756.9405	3592.2542	0.0000	1.0000
K2PI	37	-1757.1642	3592.7017	0.0000	1.0000
K2PIG	38	-1756.8311	3594.2789	0.0000	1.0000
SYMG	41	-1753.7276	3594.8449	0.0000	1.0000
SYMI	41	-1753.9930	3595.3756	0.0000	1.0000
GTR	43	-1752.0407	3596.0218	0.0000	1.0000
SYMIG	42	-1753.6078	3596.8771	0.0000	1.0000
HKY	39	-1758.1944	3599.2562	0.0000	1.0000
K2P	36	-1770.7949	3617.7264	0.0000	1.0000
SYM	40	-1767.4571	3620.0393	0.0000	1.0000
F81G	39	-1779.3186	3641.5045	0.0000	1.0000
F81I	39	-1780.9316	3644.7306	0.0000	1.0000
F81IG	40	-1780.7585	3646.6419	0.0000	1.0000
JC69G	36	-1790.0743	3656.2853	0.0000	1.0000
JC69I	36	-1791.8180	3659.7726	0.0000	1.0000
JC69IG	37	-1791.6408	3661.6549	0.0000	1.0000
F81	38	-1791.4990	3663.6149	0.0000	1.0000
JC69	35	-1802.5400	3678.9869	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1738.4840	3564.9679	0.4126	0.4126
GTRI	44	-1738.8009	3565.6017	0.3005	0.7131
GTRIG	45	-1738.3553	3566.7105	0.1726	0.8857
HKYG	40	-1744.5629	3569.1257	0.0516	0.9373
HKYI	40	-1744.7770	3569.5540	0.0417	0.9790
HKYIG	41	-1744.4610	3570.9220	0.0210	1.0000
K2PG	37	-1756.9405	3587.8809	0.0000	1.0000
K2PI	37	-1757.1642	3588.3284	0.0000	1.0000
SYMG	41	-1753.7276	3589.4553	0.0000	1.0000
K2PIG	38	-1756.8311	3589.6621	0.0000	1.0000
SYMI	41	-1753.9930	3589.9859	0.0000	1.0000
GTR	43	-1752.0407	3590.0815	0.0000	1.0000
SYMIG	42	-1753.6078	3591.2157	0.0000	1.0000
HKY	39	-1758.1944	3594.3888	0.0000	1.0000
K2P	36	-1770.7949	3613.5898	0.0000	1.0000
SYM	40	-1767.4571	3614.9143	0.0000	1.0000
F81G	39	-1779.3186	3636.6371	0.0000	1.0000
F81I	39	-1780.9316	3639.8632	0.0000	1.0000
F81IG	40	-1780.7585	3641.5169	0.0000	1.0000
JC69G	36	-1790.0743	3652.1486	0.0000	1.0000
JC69I	36	-1791.8180	3655.6359	0.0000	1.0000
JC69IG	37	-1791.6408	3657.2816	0.0000	1.0000
F81	38	-1791.4990	3658.9980	0.0000	1.0000
JC69	35	-1802.5400	3675.0799	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1744.5629	3750.0682	0.5027	0.5027
HKYI	40	-1744.7770	3750.4965	0.4058	0.9085
K2PG	37	-1756.9405	3755.2527	0.0376	0.9461
K2PI	37	-1757.1642	3755.7002	0.0301	0.9762
HKYIG	41	-1744.4610	3756.3881	0.0213	0.9975
K2PIG	38	-1756.8311	3761.5575	0.0016	0.9991
GTRG	44	-1738.4840	3764.0046	0.0005	0.9996
GTRI	44	-1738.8009	3764.6385	0.0003	1.0000
GTRIG	45	-1738.3553	3770.2708	0.0000	1.0000
HKY	39	-1758.1944	3770.8077	0.0000	1.0000
SYMG	41	-1753.7276	3774.9213	0.0000	1.0000
SYMI	41	-1753.9930	3775.4520	0.0000	1.0000
K2P	36	-1770.7949	3776.4380	0.0000	1.0000
SYMIG	42	-1753.6078	3781.2053	0.0000	1.0000
GTR	43	-1752.0407	3784.5947	0.0000	1.0000
SYM	40	-1767.4571	3795.8568	0.0000	1.0000
F81G	39	-1779.3186	3813.0561	0.0000	1.0000
JC69G	36	-1790.0743	3814.9969	0.0000	1.0000
F81I	39	-1780.9316	3816.2821	0.0000	1.0000
JC69I	36	-1791.8180	3818.4842	0.0000	1.0000
F81IG	40	-1780.7585	3822.4594	0.0000	1.0000
JC69IG	37	-1791.6408	3824.6534	0.0000	1.0000
F81	38	-1791.4990	3830.8934	0.0000	1.0000
JC69	35	-1802.5400	3833.4046	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/chr17_3028.phylip = 1 - 681;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3028.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/chr17_3028.phylip = 1 - 681;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3028.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/chr17_3028.phylip = 1 - 681;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3028.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;


-------------------------------------------------------------
End of Output

