
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/chr8_2110.phylip" (19 taxa, 418 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	-1765.6701	3629.9568	0.4403	0.4403
HKYG	40	-1770.9995	3630.6992	0.3038	0.7441
GTRIG	45	-1765.6678	3632.4646	0.1257	0.8697
HKYIG	41	-1770.9849	3633.1294	0.0901	0.9598
GTRI	44	-1768.2935	3635.2036	0.0319	0.9918
HKYI	40	-1774.6098	3637.9199	0.0082	1.0000
SYMG	41	-1786.3353	3663.8303	0.0000	1.0000
SYMIG	42	-1786.3284	3666.2888	0.0000	1.0000
K2PG	37	-1792.9925	3667.3850	0.0000	1.0000
K2PIG	38	-1792.9556	3669.7318	0.0000	1.0000
SYMI	41	-1789.4545	3670.0686	0.0000	1.0000
K2PI	37	-1796.9553	3675.3105	0.0000	1.0000
GTR	43	-1791.1673	3678.4522	0.0000	1.0000
HKY	39	-1799.1253	3684.5045	0.0000	1.0000
SYM	40	-1818.8921	3726.4844	0.0000	1.0000
K2P	36	-1826.8145	3732.6210	0.0000	1.0000
F81G	39	-1829.8423	3745.9386	0.0000	1.0000
F81IG	40	-1829.8113	3748.3229	0.0000	1.0000
F81I	39	-1837.1651	3760.5842	0.0000	1.0000
JC69G	36	-1850.5483	3780.0888	0.0000	1.0000
JC69IG	37	-1853.6101	3788.6201	0.0000	1.0000
JC69I	36	-1857.3351	3793.6622	0.0000	1.0000
F81	38	-1859.3120	3802.4447	0.0000	1.0000
JC69	35	-1882.3736	3841.3440	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1765.6701	3619.3402	0.5519	0.5519
GTRIG	45	-1765.6678	3621.3356	0.2035	0.7554
HKYG	40	-1770.9995	3621.9989	0.1461	0.9015
HKYIG	41	-1770.9849	3623.9699	0.0545	0.9560
GTRI	44	-1768.2935	3624.5870	0.0400	0.9961
HKYI	40	-1774.6098	3629.2196	0.0039	1.0000
SYMG	41	-1786.3353	3654.6707	0.0000	1.0000
SYMIG	42	-1786.3284	3656.6568	0.0000	1.0000
K2PG	37	-1792.9925	3659.9850	0.0000	1.0000
SYMI	41	-1789.4545	3660.9090	0.0000	1.0000
K2PIG	38	-1792.9556	3661.9112	0.0000	1.0000
K2PI	37	-1796.9553	3667.9105	0.0000	1.0000
GTR	43	-1791.1673	3668.3345	0.0000	1.0000
HKY	39	-1799.1253	3676.2506	0.0000	1.0000
SYM	40	-1818.8921	3717.7841	0.0000	1.0000
K2P	36	-1826.8145	3725.6289	0.0000	1.0000
F81G	39	-1829.8423	3737.6847	0.0000	1.0000
F81IG	40	-1829.8113	3739.6227	0.0000	1.0000
F81I	39	-1837.1651	3752.3303	0.0000	1.0000
JC69G	36	-1850.5483	3773.0967	0.0000	1.0000
JC69IG	37	-1853.6101	3781.2201	0.0000	1.0000
JC69I	36	-1857.3351	3786.6701	0.0000	1.0000
F81	38	-1859.3120	3794.6241	0.0000	1.0000
JC69	35	-1882.3736	3834.7472	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1770.9995	3783.4182	0.9276	0.9276
HKYIG	41	-1770.9849	3789.4246	0.0460	0.9737
HKYI	40	-1774.6098	3790.6389	0.0251	0.9988
GTRG	44	-1765.6701	3796.9014	0.0011	0.9999
GTRI	44	-1768.2935	3802.1481	0.0001	0.9999
GTRIG	45	-1765.6678	3802.9322	0.0001	1.0000
K2PG	37	-1792.9925	3809.2978	0.0000	1.0000
K2PIG	38	-1792.9556	3815.2595	0.0000	1.0000
K2PI	37	-1796.9553	3817.2234	0.0000	1.0000
SYMG	41	-1786.3353	3820.1254	0.0000	1.0000
SYMIG	42	-1786.3284	3826.1471	0.0000	1.0000
SYMI	41	-1789.4545	3826.3638	0.0000	1.0000
HKY	39	-1799.1253	3833.6344	0.0000	1.0000
GTR	43	-1791.1673	3841.8602	0.0000	1.0000
K2P	36	-1826.8145	3870.9063	0.0000	1.0000
SYM	40	-1818.8921	3879.2034	0.0000	1.0000
F81G	39	-1829.8423	3895.0685	0.0000	1.0000
F81IG	40	-1829.8113	3901.0419	0.0000	1.0000
F81I	39	-1837.1651	3909.7140	0.0000	1.0000
JC69G	36	-1850.5483	3918.3740	0.0000	1.0000
JC69IG	37	-1853.6101	3930.5330	0.0000	1.0000
JC69I	36	-1857.3351	3931.9475	0.0000	1.0000
F81	38	-1859.3120	3947.9724	0.0000	1.0000
JC69	35	-1882.3736	3975.9890	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/chr8_2110.phylip = 1 - 418;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_2110.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/chr8_2110.phylip = 1 - 418;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_2110.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/chr8_2110.phylip = 1 - 418;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_2110.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

