
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:36 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_5277.phylip" (19 taxa, 714 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	-1619.0204	3331.9601	0.4066	0.4066
GTRIG	45	-1618.1661	3332.5298	0.3058	0.7123
GTRI	44	-1619.3714	3332.6621	0.2862	0.9985
HKYG	40	-1630.0734	3345.0204	0.0006	0.9991
HKYI	40	-1630.3035	3345.4807	0.0005	0.9996
HKYIG	41	-1629.3890	3345.9029	0.0004	1.0000
SYMG	41	-1633.6282	3354.3814	0.0000	1.0000
SYMI	41	-1633.8988	3354.9226	0.0000	1.0000
SYMIG	42	-1632.9299	3355.2429	0.0000	1.0000
K2PG	37	-1641.3416	3360.8430	0.0000	1.0000
K2PI	37	-1641.5415	3361.2429	0.0000	1.0000
K2PIG	38	-1640.6782	3361.7476	0.0000	1.0000
GTR	43	-1635.8990	3363.4457	0.0000	1.0000
HKY	39	-1646.5814	3375.7919	0.0000	1.0000
F81G	39	-1648.1982	3379.0254	0.0000	1.0000
F81I	39	-1648.4418	3379.5126	0.0000	1.0000
F81IG	40	-1647.5697	3380.0132	0.0000	1.0000
SYM	40	-1649.9941	3384.8618	0.0000	1.0000
K2P	36	-1657.9778	3391.8907	0.0000	1.0000
JC69G	36	-1658.6185	3393.1719	0.0000	1.0000
JC69I	36	-1658.8506	3393.6363	0.0000	1.0000
JC69IG	37	-1658.0072	3394.1741	0.0000	1.0000
F81	38	-1664.3876	3409.1663	0.0000	1.0000
JC69	35	-1674.8157	3423.3483	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1619.0204	3326.0408	0.3890	0.3890
GTRIG	45	-1618.1661	3326.3322	0.3363	0.7253
GTRI	44	-1619.3714	3326.7428	0.2739	0.9991
HKYG	40	-1630.0734	3340.1467	0.0003	0.9995
HKYI	40	-1630.3035	3340.6070	0.0003	0.9997
HKYIG	41	-1629.3890	3340.7779	0.0002	1.0000
SYMG	41	-1633.6282	3349.2564	0.0000	1.0000
SYMI	41	-1633.8988	3349.7976	0.0000	1.0000
SYMIG	42	-1632.9299	3349.8599	0.0000	1.0000
K2PG	37	-1641.3416	3356.6832	0.0000	1.0000
K2PI	37	-1641.5415	3357.0831	0.0000	1.0000
K2PIG	38	-1640.6782	3357.3565	0.0000	1.0000
GTR	43	-1635.8990	3357.7980	0.0000	1.0000
HKY	39	-1646.5814	3371.1629	0.0000	1.0000
F81G	39	-1648.1982	3374.3964	0.0000	1.0000
F81I	39	-1648.4418	3374.8835	0.0000	1.0000
F81IG	40	-1647.5697	3375.1395	0.0000	1.0000
SYM	40	-1649.9941	3379.9881	0.0000	1.0000
K2P	36	-1657.9778	3387.9557	0.0000	1.0000
JC69G	36	-1658.6185	3389.2369	0.0000	1.0000
JC69I	36	-1658.8506	3389.7013	0.0000	1.0000
JC69IG	37	-1658.0072	3390.0143	0.0000	1.0000
F81	38	-1664.3876	3404.7751	0.0000	1.0000
JC69	35	-1674.8157	3419.6314	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1630.0734	3522.9821	0.3916	0.3916
HKYI	40	-1630.3035	3523.4423	0.3111	0.7028
K2PG	37	-1641.3416	3525.8059	0.0954	0.7982
K2PI	37	-1641.5415	3526.2058	0.0781	0.8763
GTRG	44	-1619.0204	3527.1597	0.0485	0.9248
GTRI	44	-1619.3714	3527.8617	0.0341	0.9590
HKYIG	41	-1629.3890	3528.1841	0.0291	0.9880
K2PIG	38	-1640.6782	3531.0500	0.0069	0.9950
GTRIG	45	-1618.1661	3532.0219	0.0043	0.9992
SYMG	41	-1633.6282	3536.6626	0.0004	0.9996
SYMI	41	-1633.8988	3537.2038	0.0003	1.0000
SYMIG	42	-1632.9299	3541.8369	0.0000	1.0000
HKY	39	-1646.5814	3549.4273	0.0000	1.0000
K2P	36	-1657.9778	3552.5075	0.0000	1.0000
F81G	39	-1648.1982	3552.6608	0.0000	1.0000
F81I	39	-1648.4418	3553.1480	0.0000	1.0000
JC69G	36	-1658.6185	3553.7887	0.0000	1.0000
JC69I	36	-1658.8506	3554.2531	0.0000	1.0000
GTR	43	-1635.8990	3554.3459	0.0000	1.0000
F81IG	40	-1647.5697	3557.9748	0.0000	1.0000
JC69IG	37	-1658.0072	3559.1370	0.0000	1.0000
SYM	40	-1649.9941	3562.8234	0.0000	1.0000
F81	38	-1664.3876	3578.4687	0.0000	1.0000
JC69	35	-1674.8157	3579.6123	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/chr9_5277.phylip = 1 - 714;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5277.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/chr9_5277.phylip = 1 - 714;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5277.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/chr9_5277.phylip = 1 - 714;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5277.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

