
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:07 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/chr2_2147.phylip" (19 taxa, 459 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
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
GTRI	44	-1750.4134	3598.3921	0.4857	0.4857
GTRG	44	-1750.7260	3599.0173	0.3553	0.8410
GTRIG	45	-1750.3323	3600.6889	0.1540	0.9950
HKYG	40	-1760.6616	3609.1701	0.0022	0.9973
HKYI	40	-1760.7736	3609.3941	0.0020	0.9992
HKYIG	41	-1760.5291	3611.3173	0.0008	1.0000
K2PG	37	-1773.0761	3626.8316	0.0000	1.0000
SYMG	41	-1768.8002	3627.8594	0.0000	1.0000
K2PI	37	-1773.6859	3628.0512	0.0000	1.0000
SYMI	41	-1769.2213	3628.7015	0.0000	1.0000
K2PIG	38	-1773.0420	3629.1411	0.0000	1.0000
SYMIG	42	-1768.8206	3630.3240	0.0000	1.0000
GTR	43	-1778.0979	3651.3138	0.0000	1.0000
HKY	39	-1786.4986	3658.4436	0.0000	1.0000
SYM	40	-1793.2278	3674.3024	0.0000	1.0000
K2P	36	-1798.1000	3674.5129	0.0000	1.0000
F81G	39	-1808.6485	3702.7432	0.0000	1.0000
F81I	39	-1808.8746	3703.1955	0.0000	1.0000
F81IG	40	-1808.5752	3704.9973	0.0000	1.0000
JC69G	36	-1817.0224	3712.3576	0.0000	1.0000
JC69I	36	-1817.4627	3713.2382	0.0000	1.0000
JC69IG	37	-1816.9950	3714.6694	0.0000	1.0000
F81	38	-1832.2869	3747.6310	0.0000	1.0000
JC69	35	-1840.7212	3757.3998	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1750.4134	3588.8269	0.4684	0.4684
GTRG	44	-1750.7260	3589.4521	0.3426	0.8110
GTRIG	45	-1750.3323	3590.6647	0.1869	0.9979
HKYG	40	-1760.6616	3601.3232	0.0009	0.9988
HKYI	40	-1760.7736	3601.5473	0.0008	0.9996
HKYIG	41	-1760.5291	3603.0583	0.0004	1.0000
SYMG	41	-1768.8002	3619.6004	0.0000	1.0000
K2PG	37	-1773.0761	3620.1523	0.0000	1.0000
SYMI	41	-1769.2213	3620.4425	0.0000	1.0000
K2PI	37	-1773.6859	3621.3718	0.0000	1.0000
SYMIG	42	-1768.8206	3621.6413	0.0000	1.0000
K2PIG	38	-1773.0420	3622.0840	0.0000	1.0000
GTR	43	-1778.0979	3642.1957	0.0000	1.0000
HKY	39	-1786.4986	3650.9973	0.0000	1.0000
SYM	40	-1793.2278	3666.4556	0.0000	1.0000
K2P	36	-1798.1000	3668.2001	0.0000	1.0000
F81G	39	-1808.6485	3695.2969	0.0000	1.0000
F81I	39	-1808.8746	3695.7492	0.0000	1.0000
F81IG	40	-1808.5752	3697.1504	0.0000	1.0000
JC69G	36	-1817.0224	3706.0448	0.0000	1.0000
JC69I	36	-1817.4627	3706.9254	0.0000	1.0000
JC69IG	37	-1816.9950	3707.9900	0.0000	1.0000
F81	38	-1832.2869	3740.5738	0.0000	1.0000
JC69	35	-1840.7212	3751.4424	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1760.6616	3766.4852	0.4445	0.4445
HKYI	40	-1760.7736	3766.7093	0.3974	0.8419
GTRI	44	-1750.4134	3770.5051	0.0596	0.9015
GTRG	44	-1750.7260	3771.1303	0.0436	0.9450
HKYIG	41	-1760.5291	3772.3493	0.0237	0.9687
K2PG	37	-1773.0761	3772.9271	0.0177	0.9865
K2PI	37	-1773.6859	3774.1467	0.0096	0.9961
GTRIG	45	-1750.3323	3776.4719	0.0030	0.9991
K2PIG	38	-1773.0420	3778.9879	0.0009	1.0000
SYMG	41	-1768.8002	3788.8915	0.0000	1.0000
SYMI	41	-1769.2213	3789.7336	0.0000	1.0000
SYMIG	42	-1768.8206	3795.0614	0.0000	1.0000
HKY	39	-1786.4986	3812.0302	0.0000	1.0000
K2P	36	-1798.1000	3816.8459	0.0000	1.0000
GTR	43	-1778.0979	3819.7449	0.0000	1.0000
SYM	40	-1793.2278	3831.6176	0.0000	1.0000
JC69G	36	-1817.0224	3854.6906	0.0000	1.0000
JC69I	36	-1817.4627	3855.5712	0.0000	1.0000
F81G	39	-1808.6485	3856.3299	0.0000	1.0000
F81I	39	-1808.8746	3856.7821	0.0000	1.0000
JC69IG	37	-1816.9950	3860.7649	0.0000	1.0000
F81IG	40	-1808.5752	3862.3124	0.0000	1.0000
JC69	35	-1840.7212	3895.9591	0.0000	1.0000
F81	38	-1832.2869	3897.4777	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_2147.phylip = 1 - 459;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_2147.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_2147.phylip = 1 - 459;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_2147.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr2_2147.phylip = 1 - 459;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_2147.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

