
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:34 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/chr9_5220.phylip" (19 taxa, 593 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-1631.6236	3349.1893	0.5483	0.5483
HKYIG	41	-1631.3518	3350.9540	0.2269	0.7752
GTRG	44	-1628.8088	3352.8439	0.0882	0.8634
HKYI	40	-1633.4685	3352.8791	0.0867	0.9501
GTRIG	45	-1628.5468	3354.6622	0.0355	0.9856
GTRI	44	-1630.6560	3356.5384	0.0139	0.9995
K2PG	37	-1642.6804	3364.4275	0.0003	0.9998
K2PIG	38	-1642.4091	3366.1683	0.0001	0.9999
K2PI	37	-1644.4788	3368.0242	0.0000	1.0000
SYMG	41	-1640.8744	3369.9992	0.0000	1.0000
SYMIG	42	-1640.6274	3371.8221	0.0000	1.0000
SYMI	41	-1642.6602	3373.5709	0.0000	1.0000
HKY	39	-1648.8302	3381.3023	0.0000	1.0000
GTR	43	-1646.3279	3385.5484	0.0000	1.0000
K2P	36	-1659.5918	3395.9750	0.0000	1.0000
SYM	40	-1657.9491	3401.8402	0.0000	1.0000
F81G	39	-1675.9154	3435.4728	0.0000	1.0000
F81IG	40	-1675.7986	3437.5393	0.0000	1.0000
F81I	39	-1677.0733	3437.7885	0.0000	1.0000
JC69G	36	-1684.6509	3446.0932	0.0000	1.0000
JC69IG	37	-1684.5336	3448.1338	0.0000	1.0000
JC69I	36	-1685.8212	3448.4338	0.0000	1.0000
F81	38	-1687.3312	3456.0126	0.0000	1.0000
JC69	35	-1696.1049	3466.7341	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1631.6236	3343.2473	0.4670	0.4670
HKYIG	41	-1631.3518	3344.7036	0.2255	0.6924
GTRG	44	-1628.8088	3345.6176	0.1428	0.8352
HKYI	40	-1633.4685	3346.9371	0.0738	0.9090
GTRIG	45	-1628.5468	3347.0937	0.0682	0.9772
GTRI	44	-1630.6560	3349.3121	0.0225	0.9997
K2PG	37	-1642.6804	3359.3609	0.0001	0.9999
K2PIG	38	-1642.4091	3360.8182	0.0001	0.9999
K2PI	37	-1644.4788	3362.9575	0.0000	1.0000
SYMG	41	-1640.8744	3363.7488	0.0000	1.0000
SYMIG	42	-1640.6274	3365.2548	0.0000	1.0000
SYMI	41	-1642.6602	3367.3204	0.0000	1.0000
HKY	39	-1648.8302	3375.6603	0.0000	1.0000
GTR	43	-1646.3279	3378.6558	0.0000	1.0000
K2P	36	-1659.5918	3391.1836	0.0000	1.0000
SYM	40	-1657.9491	3395.8982	0.0000	1.0000
F81G	39	-1675.9154	3429.8308	0.0000	1.0000
F81IG	40	-1675.7986	3431.5972	0.0000	1.0000
F81I	39	-1677.0733	3432.1466	0.0000	1.0000
JC69G	36	-1684.6509	3441.3018	0.0000	1.0000
JC69IG	37	-1684.5336	3443.0672	0.0000	1.0000
JC69I	36	-1685.8212	3443.6424	0.0000	1.0000
F81	38	-1687.3312	3450.6624	0.0000	1.0000
JC69	35	-1696.1049	3462.2099	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1631.6236	3518.6551	0.6712	0.6712
K2PG	37	-1642.6804	3521.6131	0.1529	0.8241
HKYI	40	-1633.4685	3522.3448	0.1061	0.9302
HKYIG	41	-1631.3518	3524.4965	0.0362	0.9664
K2PI	37	-1644.4788	3525.2097	0.0253	0.9917
K2PIG	38	-1642.4091	3527.4555	0.0082	1.0000
GTRG	44	-1628.8088	3538.5661	0.0000	1.0000
GTRI	44	-1630.6560	3542.2606	0.0000	1.0000
SYMG	41	-1640.8744	3543.5417	0.0000	1.0000
GTRIG	45	-1628.5468	3544.4274	0.0000	1.0000
HKY	39	-1648.8302	3546.6829	0.0000	1.0000
SYMI	41	-1642.6602	3547.1134	0.0000	1.0000
K2P	36	-1659.5918	3549.0506	0.0000	1.0000
SYMIG	42	-1640.6274	3549.4330	0.0000	1.0000
GTR	43	-1646.3279	3567.2192	0.0000	1.0000
SYM	40	-1657.9491	3571.3060	0.0000	1.0000
JC69G	36	-1684.6509	3599.1688	0.0000	1.0000
F81G	39	-1675.9154	3600.8534	0.0000	1.0000
JC69I	36	-1685.8212	3601.5094	0.0000	1.0000
F81I	39	-1677.0733	3603.1692	0.0000	1.0000
JC69IG	37	-1684.5336	3605.3194	0.0000	1.0000
F81IG	40	-1675.7986	3607.0050	0.0000	1.0000
JC69	35	-1696.1049	3615.6917	0.0000	1.0000
F81	38	-1687.3312	3617.2998	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5220.phylip = 1 - 593;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5220.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5220.phylip = 1 - 593;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5220.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;


[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/chr9_5220.phylip = 1 - 593;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5220.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

