
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:26 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/chr5_1725.phylip" (19 taxa, 603 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	-1567.1601	3229.4170	0.5182	0.5182
GTRI	44	-1567.6737	3230.4442	0.3100	0.8282
GTRIG	45	-1567.1128	3231.6583	0.1690	0.9972
GTR	43	-1574.2769	3241.3231	0.0013	0.9985
HKYG	40	-1578.3085	3242.4534	0.0008	0.9993
HKYI	40	-1578.7797	3243.3957	0.0005	0.9997
HKYIG	41	-1578.2655	3244.6700	0.0003	1.0000
HKY	39	-1584.9172	3253.3762	0.0000	1.0000
F81G	39	-1589.4986	3262.5390	0.0000	1.0000
F81I	39	-1589.9522	3263.4461	0.0000	1.0000
F81IG	40	-1589.4655	3264.7673	0.0000	1.0000
F81	38	-1595.6850	3272.6253	0.0000	1.0000
SYMG	41	-1595.8453	3279.8296	0.0000	1.0000
SYMI	41	-1596.3841	3280.9072	0.0000	1.0000
SYMIG	42	-1595.8151	3282.0802	0.0000	1.0000
K2PG	37	-1602.9495	3284.8760	0.0000	1.0000
K2PI	37	-1603.4666	3285.9101	0.0000	1.0000
K2PIG	38	-1602.9097	3287.0747	0.0000	1.0000
SYM	40	-1601.8740	3289.5843	0.0000	1.0000
K2P	36	-1609.3341	3295.3750	0.0000	1.0000
JC69G	36	-1611.8582	3300.4230	0.0000	1.0000
JC69I	36	-1612.3428	3301.3924	0.0000	1.0000
JC69IG	37	-1611.8256	3302.6282	0.0000	1.0000
JC69	35	-1618.0183	3310.4810	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1567.1601	3222.3202	0.5031	0.5031
GTRI	44	-1567.6737	3223.3474	0.3010	0.8041
GTRIG	45	-1567.1128	3224.2257	0.1940	0.9981
GTR	43	-1574.2769	3234.5539	0.0011	0.9992
HKYG	40	-1578.3085	3236.6171	0.0004	0.9996
HKYI	40	-1578.7797	3237.5594	0.0002	0.9998
HKYIG	41	-1578.2655	3238.5309	0.0002	1.0000
HKY	39	-1584.9172	3247.8345	0.0000	1.0000
F81G	39	-1589.4986	3256.9973	0.0000	1.0000
F81I	39	-1589.9522	3257.9043	0.0000	1.0000
F81IG	40	-1589.4655	3258.9310	0.0000	1.0000
F81	38	-1595.6850	3267.3700	0.0000	1.0000
SYMG	41	-1595.8453	3273.6906	0.0000	1.0000
SYMI	41	-1596.3841	3274.7681	0.0000	1.0000
SYMIG	42	-1595.8151	3275.6302	0.0000	1.0000
K2PG	37	-1602.9495	3279.8990	0.0000	1.0000
K2PI	37	-1603.4666	3280.9331	0.0000	1.0000
K2PIG	38	-1602.9097	3281.8194	0.0000	1.0000
SYM	40	-1601.8740	3283.7480	0.0000	1.0000
K2P	36	-1609.3341	3290.6683	0.0000	1.0000
JC69G	36	-1611.8582	3295.7163	0.0000	1.0000
JC69I	36	-1612.3428	3296.6856	0.0000	1.0000
JC69IG	37	-1611.8256	3297.6512	0.0000	1.0000
JC69	35	-1618.0183	3306.0365	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1578.3085	3412.6938	0.4956	0.4956
HKYI	40	-1578.7797	3413.6361	0.3094	0.8050
GTRG	44	-1567.1601	3416.0046	0.0947	0.8997
GTRI	44	-1567.6737	3417.0318	0.0566	0.9563
HKYIG	41	-1578.2655	3419.0095	0.0211	0.9774
HKY	39	-1584.9172	3419.5093	0.0164	0.9938
GTRIG	45	-1567.1128	3422.3119	0.0040	0.9978
GTR	43	-1574.2769	3423.8363	0.0019	0.9997
F81G	39	-1589.4986	3428.6721	0.0002	0.9999
F81I	39	-1589.9522	3429.5791	0.0001	1.0000
F81	38	-1595.6850	3434.6429	0.0000	1.0000
F81IG	40	-1589.4655	3435.0077	0.0000	1.0000
K2PG	37	-1602.9495	3442.7699	0.0000	1.0000
K2PI	37	-1603.4666	3443.8040	0.0000	1.0000
K2PIG	38	-1602.9097	3449.0923	0.0000	1.0000
K2P	36	-1609.3341	3449.1373	0.0000	1.0000
SYMG	41	-1595.8453	3454.1692	0.0000	1.0000
JC69G	36	-1611.8582	3454.1853	0.0000	1.0000
JC69I	36	-1612.3428	3455.1547	0.0000	1.0000
SYMI	41	-1596.3841	3455.2467	0.0000	1.0000
SYM	40	-1601.8740	3459.8247	0.0000	1.0000
JC69	35	-1618.0183	3460.1036	0.0000	1.0000
SYMIG	42	-1595.8151	3460.5107	0.0000	1.0000
JC69IG	37	-1611.8256	3460.5222	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/chr5_1725.phylip = 1 - 603;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1725.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/chr5_1725.phylip = 1 - 603;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1725.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/chr5_1725.phylip = 1 - 603;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1725.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

