
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:48 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/chr2_11743.phylip" (19 taxa, 495 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-1529.5075	3155.8149	0.3323	0.3323
GTRIG	45	-1528.5683	3156.3571	0.2534	0.5857
SYMG	41	-1533.9518	3157.5063	0.1426	0.7283
SYMIG	42	-1532.9715	3157.9343	0.1152	0.8435
HKYG	40	-1536.2737	3159.7721	0.0459	0.8894
GTRI	44	-1531.5520	3159.9040	0.0430	0.9324
HKYIG	41	-1535.3963	3160.3953	0.0336	0.9661
SYMI	41	-1536.6132	3162.8291	0.0100	0.9760
K2PG	37	-1541.3771	3162.9073	0.0096	0.9856
K2PIG	38	-1540.4931	3163.4863	0.0072	0.9928
HKYI	40	-1538.3448	3163.9144	0.0058	0.9986
K2PI	37	-1543.2928	3166.7388	0.0014	1.0000
SYM	40	-1569.2398	3225.7043	0.0000	1.0000
GTR	43	-1565.8404	3226.0710	0.0000	1.0000
HKY	39	-1572.0080	3228.8732	0.0000	1.0000
K2P	36	-1577.8306	3233.4779	0.0000	1.0000
F81G	39	-1579.6107	3244.0786	0.0000	1.0000
F81IG	40	-1578.6922	3244.6091	0.0000	1.0000
F81I	39	-1581.3621	3247.5814	0.0000	1.0000
JC69G	36	-1587.9380	3253.6927	0.0000	1.0000
JC69IG	37	-1587.0702	3254.2935	0.0000	1.0000
JC69I	36	-1589.8679	3257.5524	0.0000	1.0000
F81	38	-1615.2050	3312.9100	0.0000	1.0000
JC69	35	-1622.1828	3319.8558	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1529.5075	3147.0149	0.3709	0.3709
GTRIG	45	-1528.5683	3147.1366	0.3490	0.7199
SYMG	41	-1533.9518	3149.9037	0.0875	0.8074
SYMIG	42	-1532.9715	3149.9431	0.0858	0.8932
GTRI	44	-1531.5520	3151.1040	0.0480	0.9412
HKYG	40	-1536.2737	3152.5475	0.0233	0.9645
HKYIG	41	-1535.3963	3152.7926	0.0206	0.9851
SYMI	41	-1536.6132	3155.2264	0.0061	0.9913
HKYI	40	-1538.3448	3156.6897	0.0029	0.9942
K2PG	37	-1541.3771	3156.7541	0.0028	0.9970
K2PIG	38	-1540.4931	3156.9863	0.0025	0.9996
K2PI	37	-1543.2928	3160.5856	0.0004	1.0000
GTR	43	-1565.8404	3217.6807	0.0000	1.0000
SYM	40	-1569.2398	3218.4797	0.0000	1.0000
HKY	39	-1572.0080	3222.0161	0.0000	1.0000
K2P	36	-1577.8306	3227.6613	0.0000	1.0000
F81G	39	-1579.6107	3237.2214	0.0000	1.0000
F81IG	40	-1578.6922	3237.3845	0.0000	1.0000
F81I	39	-1581.3621	3240.7242	0.0000	1.0000
JC69G	36	-1587.9380	3247.8761	0.0000	1.0000
JC69IG	37	-1587.0702	3248.1403	0.0000	1.0000
JC69I	36	-1589.8679	3251.7358	0.0000	1.0000
F81	38	-1615.2050	3306.4100	0.0000	1.0000
JC69	35	-1622.1828	3314.3656	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1541.3771	3312.3228	0.7796	0.7796
K2PI	37	-1543.2928	3316.1543	0.1148	0.8944
K2PIG	38	-1540.4931	3316.7595	0.0848	0.9792
HKYG	40	-1536.2737	3320.7298	0.0116	0.9909
SYMG	41	-1533.9518	3322.2905	0.0053	0.9962
HKYI	40	-1538.3448	3324.8720	0.0015	0.9977
HKYIG	41	-1535.3963	3325.1795	0.0013	0.9989
SYMIG	42	-1532.9715	3326.5345	0.0006	0.9996
SYMI	41	-1536.6132	3327.6133	0.0004	0.9999
GTRG	44	-1529.5075	3332.0154	0.0000	1.0000
GTRI	44	-1531.5520	3336.1045	0.0000	1.0000
GTRIG	45	-1528.5683	3336.3417	0.0000	1.0000
K2P	36	-1577.8306	3379.0254	0.0000	1.0000
HKY	39	-1572.0080	3385.9938	0.0000	1.0000
SYM	40	-1569.2398	3386.6620	0.0000	1.0000
GTR	43	-1565.8404	3398.4767	0.0000	1.0000
JC69G	36	-1587.9380	3399.2401	0.0000	1.0000
F81G	39	-1579.6107	3401.1992	0.0000	1.0000
JC69I	36	-1589.8679	3403.0999	0.0000	1.0000
JC69IG	37	-1587.0702	3403.7089	0.0000	1.0000
F81I	39	-1581.3621	3404.7020	0.0000	1.0000
F81IG	40	-1578.6922	3405.5668	0.0000	1.0000
JC69	35	-1622.1828	3461.5251	0.0000	1.0000
F81	38	-1615.2050	3466.1832	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/chr2_11743.phylip = 1 - 495;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11743.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/chr2_11743.phylip = 1 - 495;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11743.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11743.phylip = 1 - 495;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11743.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

