
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:15 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/chr1_28829.phylip" (19 taxa, 669 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-1747.8096	3592.2644	0.7388	0.7388
GTRG	44	-1750.2723	3594.8908	0.1987	0.9375
GTRI	44	-1751.4306	3597.2073	0.0624	0.9999
HKYIG	41	-1761.6915	3610.8758	0.0001	0.9999
HKYG	40	-1763.2569	3611.7368	0.0000	1.0000
HKYI	40	-1763.9874	3613.1977	0.0000	1.0000
SYMIG	42	-1776.9912	3643.7523	0.0000	1.0000
SYMG	41	-1778.6742	3644.8411	0.0000	1.0000
SYMI	41	-1779.4145	3646.3218	0.0000	1.0000
K2PIG	38	-1783.3513	3647.4073	0.0000	1.0000
K2PG	37	-1784.8770	3648.2104	0.0000	1.0000
K2PI	37	-1785.5707	3649.5978	0.0000	1.0000
F81IG	40	-1783.6804	3652.5837	0.0000	1.0000
F81G	39	-1785.0809	3653.1220	0.0000	1.0000
F81I	39	-1785.7401	3654.4405	0.0000	1.0000
GTR	43	-1784.3504	3660.7553	0.0000	1.0000
HKY	39	-1793.9964	3670.9531	0.0000	1.0000
JC69IG	37	-1805.4443	3689.3450	0.0000	1.0000
JC69G	36	-1806.9119	3690.0389	0.0000	1.0000
JC69I	36	-1807.5303	3691.2757	0.0000	1.0000
K2P	36	-1814.7769	3705.7691	0.0000	1.0000
SYM	40	-1811.1964	3707.6158	0.0000	1.0000
F81	38	-1815.4584	3711.6215	0.0000	1.0000
JC69	35	-1838.7774	3751.5358	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1747.8096	3585.6192	0.7666	0.7666
GTRG	44	-1750.2723	3588.5447	0.1775	0.9442
GTRI	44	-1751.4306	3590.8612	0.0558	0.9999
HKYIG	41	-1761.6915	3605.3830	0.0000	1.0000
HKYG	40	-1763.2569	3606.5138	0.0000	1.0000
HKYI	40	-1763.9874	3607.9748	0.0000	1.0000
SYMIG	42	-1776.9912	3637.9823	0.0000	1.0000
SYMG	41	-1778.6742	3639.3483	0.0000	1.0000
SYMI	41	-1779.4145	3640.8290	0.0000	1.0000
K2PIG	38	-1783.3513	3642.7025	0.0000	1.0000
K2PG	37	-1784.8770	3643.7539	0.0000	1.0000
K2PI	37	-1785.5707	3645.1413	0.0000	1.0000
F81IG	40	-1783.6804	3647.3608	0.0000	1.0000
F81G	39	-1785.0809	3648.1617	0.0000	1.0000
F81I	39	-1785.7401	3649.4802	0.0000	1.0000
GTR	43	-1784.3504	3654.7009	0.0000	1.0000
HKY	39	-1793.9964	3665.9929	0.0000	1.0000
JC69IG	37	-1805.4443	3684.8886	0.0000	1.0000
JC69G	36	-1806.9119	3685.8238	0.0000	1.0000
JC69I	36	-1807.5303	3687.0605	0.0000	1.0000
K2P	36	-1814.7769	3701.5539	0.0000	1.0000
SYM	40	-1811.1964	3702.3928	0.0000	1.0000
F81	38	-1815.4584	3706.9167	0.0000	1.0000
JC69	35	-1838.7774	3747.5547	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1763.2569	3786.7452	0.2952	0.2952
GTRG	44	-1750.2723	3786.7992	0.2873	0.5826
HKYI	40	-1763.9874	3788.2061	0.1422	0.7248
GTRIG	45	-1747.8096	3788.3794	0.1304	0.8551
GTRI	44	-1751.4306	3789.1157	0.0902	0.9454
HKYIG	41	-1761.6915	3790.1201	0.0546	1.0000
K2PG	37	-1784.8770	3810.4680	0.0000	1.0000
K2PI	37	-1785.5707	3811.8554	0.0000	1.0000
K2PIG	38	-1783.3513	3813.9223	0.0000	1.0000
F81G	39	-1785.0809	3823.8873	0.0000	1.0000
SYMG	41	-1778.6742	3824.0854	0.0000	1.0000
F81I	39	-1785.7401	3825.2058	0.0000	1.0000
SYMI	41	-1779.4145	3825.5661	0.0000	1.0000
SYMIG	42	-1776.9912	3827.2253	0.0000	1.0000
F81IG	40	-1783.6804	3827.5922	0.0000	1.0000
HKY	39	-1793.9964	3841.7184	0.0000	1.0000
JC69G	36	-1806.9119	3848.0320	0.0000	1.0000
GTR	43	-1784.3504	3848.4496	0.0000	1.0000
JC69I	36	-1807.5303	3849.2688	0.0000	1.0000
JC69IG	37	-1805.4443	3851.6026	0.0000	1.0000
K2P	36	-1814.7769	3863.7621	0.0000	1.0000
F81	38	-1815.4584	3878.1365	0.0000	1.0000
SYM	40	-1811.1964	3882.6242	0.0000	1.0000
JC69	35	-1838.7774	3905.2572	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28829.phylip = 1 - 669;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28829.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28829.phylip = 1 - 669;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28829.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) 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/chr1_28829.phylip = 1 - 669;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28829.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

