
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:57 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_7957.phylip" (19 taxa, 665 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-1697.1925	3488.7721	0.3049	0.3049
GTRI	44	-1697.3198	3489.0266	0.2684	0.5733
GTRIG	45	-1696.3541	3489.3964	0.2231	0.7965
HKYIG	41	-1702.0947	3491.7174	0.0699	0.8664
HKYG	40	-1703.4856	3492.2277	0.0542	0.9205
HKYI	40	-1703.8290	3492.9144	0.0384	0.9590
SYMG	41	-1703.4029	3494.3339	0.0189	0.9779
K2PIG	38	-1707.7678	3496.2703	0.0072	0.9850
K2PG	37	-1709.0681	3496.6210	0.0060	0.9911
K2PI	37	-1709.4390	3497.3629	0.0042	0.9952
SYMI	41	-1705.2477	3498.0234	0.0030	0.9982
SYMIG	42	-1704.6146	3499.0364	0.0018	1.0000
F81IG	40	-1726.5263	3538.3090	0.0000	1.0000
F81G	39	-1727.7490	3538.4900	0.0000	1.0000
F81I	39	-1728.1909	3539.3739	0.0000	1.0000
JC69IG	37	-1731.0910	3540.6668	0.0000	1.0000
JC69G	36	-1732.2572	3540.7564	0.0000	1.0000
JC69I	36	-1732.7121	3541.6662	0.0000	1.0000
HKY	39	-1733.5983	3550.1887	0.0000	1.0000
GTR	43	-1730.3044	3552.7022	0.0000	1.0000
K2P	36	-1738.5885	3553.4191	0.0000	1.0000
SYM	40	-1736.3929	3558.0423	0.0000	1.0000
F81	38	-1756.0389	3592.8126	0.0000	1.0000
JC69	35	-1760.2264	3594.4591	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1697.1925	3482.3850	0.3198	0.3198
GTRI	44	-1697.3198	3482.6395	0.2815	0.6013
GTRIG	45	-1696.3541	3482.7082	0.2720	0.8733
HKYIG	41	-1702.0947	3486.1893	0.0477	0.9211
HKYG	40	-1703.4856	3486.9713	0.0323	0.9533
HKYI	40	-1703.8290	3487.6580	0.0229	0.9762
SYMG	41	-1703.4029	3488.8058	0.0129	0.9891
K2PIG	38	-1707.7678	3491.5355	0.0033	0.9924
K2PG	37	-1709.0681	3492.1362	0.0024	0.9949
SYMI	41	-1705.2477	3492.4953	0.0020	0.9969
K2PI	37	-1709.4390	3492.8781	0.0017	0.9986
SYMIG	42	-1704.6146	3493.2293	0.0014	1.0000
F81IG	40	-1726.5263	3533.0525	0.0000	1.0000
F81G	39	-1727.7490	3533.4980	0.0000	1.0000
F81I	39	-1728.1909	3534.3819	0.0000	1.0000
JC69IG	37	-1731.0910	3536.1820	0.0000	1.0000
JC69G	36	-1732.2572	3536.5143	0.0000	1.0000
JC69I	36	-1732.7121	3537.4242	0.0000	1.0000
HKY	39	-1733.5983	3545.1967	0.0000	1.0000
GTR	43	-1730.3044	3546.6088	0.0000	1.0000
K2P	36	-1738.5885	3549.1770	0.0000	1.0000
SYM	40	-1736.3929	3552.7859	0.0000	1.0000
F81	38	-1756.0389	3588.0777	0.0000	1.0000
JC69	35	-1760.2264	3590.4527	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1709.0681	3658.6283	0.5370	0.5370
K2PI	37	-1709.4390	3659.3702	0.3706	0.9076
K2PIG	38	-1707.7678	3662.5274	0.0764	0.9840
HKYG	40	-1703.4856	3666.9628	0.0083	0.9924
HKYI	40	-1703.8290	3667.6495	0.0059	0.9983
HKYIG	41	-1702.0947	3670.6806	0.0013	0.9996
SYMG	41	-1703.4029	3673.2971	0.0004	0.9999
SYMI	41	-1705.2477	3676.9866	0.0001	1.0000
GTRG	44	-1697.1925	3680.3756	0.0000	1.0000
GTRI	44	-1697.3198	3680.6302	0.0000	1.0000
SYMIG	42	-1704.6146	3682.2203	0.0000	1.0000
GTRIG	45	-1696.3541	3685.1986	0.0000	1.0000
JC69G	36	-1732.2572	3698.5067	0.0000	1.0000
JC69I	36	-1732.7121	3699.4165	0.0000	1.0000
JC69IG	37	-1731.0910	3702.6741	0.0000	1.0000
F81G	39	-1727.7490	3708.9897	0.0000	1.0000
F81I	39	-1728.1909	3709.8736	0.0000	1.0000
K2P	36	-1738.5885	3711.1694	0.0000	1.0000
F81IG	40	-1726.5263	3713.0440	0.0000	1.0000
HKY	39	-1733.5983	3720.6884	0.0000	1.0000
SYM	40	-1736.3929	3732.7774	0.0000	1.0000
GTR	43	-1730.3044	3740.0996	0.0000	1.0000
JC69	35	-1760.2264	3747.9453	0.0000	1.0000
F81	38	-1756.0389	3759.0696	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/chr2_7957.phylip = 1 - 665;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7957.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/chr2_7957.phylip = 1 - 665;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7957.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7957.phylip = 1 - 665;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7957.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

