
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:08 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_32248.phylip" (19 taxa, 679 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	-1634.3246	3362.8953	0.3867	0.3867
GTRIG	45	-1633.5863	3363.7129	0.2569	0.6437
GTRI	44	-1634.8607	3363.9674	0.2262	0.8699
HKYG	40	-1640.8325	3366.8061	0.0547	0.9246
HKYI	40	-1641.0256	3367.1923	0.0451	0.9698
HKYIG	41	-1640.2929	3367.9925	0.0302	1.0000
GTR	43	-1657.3834	3406.7258	0.0000	1.0000
HKY	39	-1665.5355	3413.9535	0.0000	1.0000
F81G	39	-1670.6378	3424.1581	0.0000	1.0000
F81I	39	-1672.6129	3428.1084	0.0000	1.0000
F81IG	40	-1672.2700	3429.6810	0.0000	1.0000
K2PG	37	-1684.8246	3448.0361	0.0000	1.0000
K2PI	37	-1684.8401	3448.0671	0.0000	1.0000
K2PIG	38	-1684.6107	3449.8527	0.0000	1.0000
SYMG	41	-1682.4002	3452.2069	0.0000	1.0000
SYMI	41	-1682.4985	3452.4036	0.0000	1.0000
SYMIG	42	-1682.0876	3453.8545	0.0000	1.0000
F81	38	-1697.7588	3476.1489	0.0000	1.0000
SYM	40	-1707.0231	3499.1872	0.0000	1.0000
K2P	36	-1711.9257	3500.0009	0.0000	1.0000
JC69G	36	-1712.6130	3501.3755	0.0000	1.0000
JC69I	36	-1712.6384	3501.4263	0.0000	1.0000
JC69IG	37	-1712.5061	3503.3991	0.0000	1.0000
JC69	35	-1738.6966	3551.3124	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1634.3246	3356.6492	0.3914	0.3914
GTRIG	45	-1633.5863	3357.1727	0.3013	0.6927
GTRI	44	-1634.8607	3357.7214	0.2290	0.9217
HKYG	40	-1640.8325	3361.6650	0.0319	0.9536
HKYI	40	-1641.0256	3362.0513	0.0263	0.9799
HKYIG	41	-1640.2929	3362.5859	0.0201	1.0000
GTR	43	-1657.3834	3400.7667	0.0000	1.0000
HKY	39	-1665.5355	3409.0709	0.0000	1.0000
F81G	39	-1670.6378	3419.2755	0.0000	1.0000
F81I	39	-1672.6129	3423.2258	0.0000	1.0000
F81IG	40	-1672.2700	3424.5399	0.0000	1.0000
K2PG	37	-1684.8246	3443.6492	0.0000	1.0000
K2PI	37	-1684.8401	3443.6802	0.0000	1.0000
K2PIG	38	-1684.6107	3445.2214	0.0000	1.0000
SYMG	41	-1682.4002	3446.8003	0.0000	1.0000
SYMI	41	-1682.4985	3446.9970	0.0000	1.0000
SYMIG	42	-1682.0876	3448.1752	0.0000	1.0000
F81	38	-1697.7588	3471.5177	0.0000	1.0000
SYM	40	-1707.0231	3494.0461	0.0000	1.0000
K2P	36	-1711.9257	3495.8514	0.0000	1.0000
JC69G	36	-1712.6130	3497.2259	0.0000	1.0000
JC69I	36	-1712.6384	3497.2767	0.0000	1.0000
JC69IG	37	-1712.5061	3499.0122	0.0000	1.0000
JC69	35	-1738.6966	3547.3933	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1640.8325	3542.4899	0.5284	0.5284
HKYI	40	-1641.0256	3542.8761	0.4356	0.9639
HKYIG	41	-1640.2929	3547.9313	0.0348	0.9987
GTRG	44	-1634.3246	3555.5565	0.0008	0.9995
GTRI	44	-1634.8607	3556.6287	0.0004	0.9999
GTRIG	45	-1633.5863	3560.6006	0.0001	1.0000
HKY	39	-1665.5355	3585.3751	0.0000	1.0000
GTR	43	-1657.3834	3595.1534	0.0000	1.0000
F81G	39	-1670.6378	3595.5797	0.0000	1.0000
F81I	39	-1672.6129	3599.5300	0.0000	1.0000
F81IG	40	-1672.2700	3605.3648	0.0000	1.0000
K2PG	37	-1684.8246	3610.9122	0.0000	1.0000
K2PI	37	-1684.8401	3610.9431	0.0000	1.0000
K2PIG	38	-1684.6107	3617.0050	0.0000	1.0000
SYMG	41	-1682.4002	3632.1458	0.0000	1.0000
SYMI	41	-1682.4985	3632.3425	0.0000	1.0000
SYMIG	42	-1682.0876	3638.0413	0.0000	1.0000
F81	38	-1697.7588	3643.3013	0.0000	1.0000
K2P	36	-1711.9257	3658.5938	0.0000	1.0000
JC69G	36	-1712.6130	3659.9683	0.0000	1.0000
JC69I	36	-1712.6384	3660.0191	0.0000	1.0000
JC69IG	37	-1712.5061	3666.2752	0.0000	1.0000
SYM	40	-1707.0231	3674.8710	0.0000	1.0000
JC69	35	-1738.6966	3705.6150	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/chr1_32248.phylip = 1 - 679;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32248.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/chr1_32248.phylip = 1 - 679;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32248.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/chr1_32248.phylip = 1 - 679;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32248.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

