
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:28 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/chr4_6508.phylip" (19 taxa, 378 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	-1631.9833	3363.8584	0.7729	0.7729
GTRIG	45	-1631.9826	3366.4352	0.2131	0.9860
GTRI	44	-1636.1984	3372.2887	0.0114	0.9974
HKYG	40	-1643.0164	3375.7658	0.0020	0.9994
HKYIG	41	-1643.0162	3378.2824	0.0006	0.9999
HKYI	40	-1646.7085	3383.1499	0.0001	1.0000
GTR	43	-1647.7301	3392.7895	0.0000	1.0000
HKY	39	-1658.1558	3403.5424	0.0000	1.0000
K2PG	37	-1665.2876	3412.8457	0.0000	1.0000
K2PIG	38	-1665.2873	3415.3180	0.0000	1.0000
SYMG	41	-1661.5893	3415.4286	0.0000	1.0000
SYMIG	42	-1661.5892	3417.9604	0.0000	1.0000
K2PI	37	-1668.6532	3419.5769	0.0000	1.0000
SYMI	41	-1664.2556	3420.7612	0.0000	1.0000
SYM	40	-1675.3054	3440.3438	0.0000	1.0000
K2P	36	-1680.9259	3441.6641	0.0000	1.0000
F81G	39	-1684.3784	3455.9876	0.0000	1.0000
F81IG	40	-1684.3782	3458.4893	0.0000	1.0000
F81I	39	-1686.6196	3460.4699	0.0000	1.0000
F81	38	-1695.9308	3476.6049	0.0000	1.0000
JC69G	36	-1700.3492	3480.5106	0.0000	1.0000
JC69IG	37	-1700.3490	3482.9687	0.0000	1.0000
JC69I	36	-1702.4059	3484.6242	0.0000	1.0000
JC69	35	-1713.0366	3503.4416	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1631.9833	3351.9665	0.7225	0.7225
GTRIG	45	-1631.9826	3353.9653	0.2660	0.9884
GTRI	44	-1636.1984	3360.3968	0.0107	0.9991
HKYG	40	-1643.0164	3366.0328	0.0006	0.9997
HKYIG	41	-1643.0162	3368.0324	0.0002	1.0000
HKYI	40	-1646.7085	3373.4170	0.0000	1.0000
GTR	43	-1647.7301	3381.4602	0.0000	1.0000
HKY	39	-1658.1558	3394.3116	0.0000	1.0000
K2PG	37	-1665.2876	3404.5751	0.0000	1.0000
SYMG	41	-1661.5893	3405.1786	0.0000	1.0000
K2PIG	38	-1665.2873	3406.5747	0.0000	1.0000
SYMIG	42	-1661.5892	3407.1783	0.0000	1.0000
SYMI	41	-1664.2556	3410.5112	0.0000	1.0000
K2PI	37	-1668.6532	3411.3063	0.0000	1.0000
SYM	40	-1675.3054	3430.6108	0.0000	1.0000
K2P	36	-1680.9259	3433.8518	0.0000	1.0000
F81G	39	-1684.3784	3446.7569	0.0000	1.0000
F81IG	40	-1684.3782	3448.7564	0.0000	1.0000
F81I	39	-1686.6196	3451.2392	0.0000	1.0000
F81	38	-1695.9308	3467.8615	0.0000	1.0000
JC69G	36	-1700.3492	3472.6983	0.0000	1.0000
JC69IG	37	-1700.3490	3474.6981	0.0000	1.0000
JC69I	36	-1702.4059	3476.8119	0.0000	1.0000
JC69	35	-1713.0366	3496.0732	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1643.0164	3523.4286	0.6501	0.6501
GTRG	44	-1631.9833	3525.1019	0.2816	0.9317
HKYIG	41	-1643.0162	3529.3631	0.0334	0.9651
HKYI	40	-1646.7085	3530.8127	0.0162	0.9813
GTRIG	45	-1631.9826	3531.0355	0.0145	0.9958
GTRI	44	-1636.1984	3533.5321	0.0042	1.0000
HKY	39	-1658.1558	3547.7725	0.0000	1.0000
K2PG	37	-1665.2876	3550.1662	0.0000	1.0000
GTR	43	-1647.7301	3550.6607	0.0000	1.0000
K2PIG	38	-1665.2873	3556.1007	0.0000	1.0000
K2PI	37	-1668.6532	3556.8974	0.0000	1.0000
SYMG	41	-1661.5893	3566.5093	0.0000	1.0000
SYMI	41	-1664.2556	3571.8419	0.0000	1.0000
SYMIG	42	-1661.5892	3572.4439	0.0000	1.0000
K2P	36	-1680.9259	3575.5080	0.0000	1.0000
SYM	40	-1675.3054	3588.0066	0.0000	1.0000
F81G	39	-1684.3784	3600.2177	0.0000	1.0000
F81I	39	-1686.6196	3604.7000	0.0000	1.0000
F81IG	40	-1684.3782	3606.1522	0.0000	1.0000
JC69G	36	-1700.3492	3614.3545	0.0000	1.0000
F81	38	-1695.9308	3617.3875	0.0000	1.0000
JC69I	36	-1702.4059	3618.4681	0.0000	1.0000
JC69IG	37	-1700.3490	3620.2892	0.0000	1.0000
JC69	35	-1713.0366	3633.7945	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/chr4_6508.phylip = 1 - 378;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_6508.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/chr4_6508.phylip = 1 - 378;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_6508.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/chr4_6508.phylip = 1 - 378;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_6508.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

