
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:01 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/chr8_4319.phylip" (19 taxa, 384 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	-1595.4330	3290.5474	0.4452	0.4452
HKYG	40	-1600.6558	3290.8743	0.3780	0.8232
HKYIG	41	-1600.8431	3293.7564	0.0895	0.9127
GTRIG	45	-1595.7937	3293.8358	0.0860	0.9987
HKYI	40	-1606.4258	3302.4142	0.0012	0.9999
GTRI	44	-1603.6026	3306.8867	0.0001	1.0000
K2PG	37	-1618.4048	3318.9367	0.0000	1.0000
K2PIG	38	-1618.2823	3321.1559	0.0000	1.0000
SYMG	41	-1616.9939	3326.0580	0.0000	1.0000
K2PI	37	-1622.8345	3327.7961	0.0000	1.0000
SYMIG	42	-1616.8855	3328.3635	0.0000	1.0000
SYMI	41	-1621.8760	3335.8221	0.0000	1.0000
HKY	39	-1628.0465	3343.1627	0.0000	1.0000
GTR	43	-1624.2801	3345.6895	0.0000	1.0000
K2P	36	-1644.7377	3369.1527	0.0000	1.0000
SYM	40	-1643.0058	3375.5742	0.0000	1.0000
F81G	39	-1648.8781	3384.8260	0.0000	1.0000
F81IG	40	-1648.8473	3387.2572	0.0000	1.0000
F81I	39	-1652.5812	3392.2321	0.0000	1.0000
JC69G	36	-1661.4812	3402.6396	0.0000	1.0000
JC69IG	37	-1661.4317	3404.9906	0.0000	1.0000
JC69I	36	-1665.1120	3409.9012	0.0000	1.0000
F81	38	-1673.6329	3431.8571	0.0000	1.0000
JC69	35	-1685.8038	3448.8489	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1595.4330	3278.8660	0.6091	0.6091
HKYG	40	-1600.6558	3281.3116	0.1793	0.7884
GTRIG	45	-1595.7937	3281.5873	0.1562	0.9446
HKYIG	41	-1600.8431	3283.6862	0.0547	0.9993
HKYI	40	-1606.4258	3292.8516	0.0006	0.9998
GTRI	44	-1603.6026	3295.2053	0.0002	1.0000
K2PG	37	-1618.4048	3310.8095	0.0000	1.0000
K2PIG	38	-1618.2823	3312.5646	0.0000	1.0000
SYMG	41	-1616.9939	3315.9878	0.0000	1.0000
SYMIG	42	-1616.8855	3317.7711	0.0000	1.0000
K2PI	37	-1622.8345	3319.6690	0.0000	1.0000
SYMI	41	-1621.8760	3325.7519	0.0000	1.0000
HKY	39	-1628.0465	3334.0930	0.0000	1.0000
GTR	43	-1624.2801	3334.5601	0.0000	1.0000
K2P	36	-1644.7377	3361.4754	0.0000	1.0000
SYM	40	-1643.0058	3366.0115	0.0000	1.0000
F81G	39	-1648.8781	3375.7562	0.0000	1.0000
F81IG	40	-1648.8473	3377.6945	0.0000	1.0000
F81I	39	-1652.5812	3383.1623	0.0000	1.0000
JC69G	36	-1661.4812	3394.9624	0.0000	1.0000
JC69IG	37	-1661.4317	3396.8635	0.0000	1.0000
JC69I	36	-1665.1120	3402.2239	0.0000	1.0000
F81	38	-1673.6329	3423.2658	0.0000	1.0000
JC69	35	-1685.8038	3441.6075	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1600.6558	3439.3373	0.9552	0.9552
HKYIG	41	-1600.8431	3445.6625	0.0404	0.9956
HKYI	40	-1606.4258	3450.8773	0.0030	0.9986
GTRG	44	-1595.4330	3452.6943	0.0012	0.9998
K2PG	37	-1618.4048	3456.9833	0.0001	0.9999
GTRIG	45	-1595.7937	3459.3662	0.0000	1.0000
K2PIG	38	-1618.2823	3462.6891	0.0000	1.0000
K2PI	37	-1622.8345	3465.8427	0.0000	1.0000
GTRI	44	-1603.6026	3469.0336	0.0000	1.0000
SYMG	41	-1616.9939	3477.9641	0.0000	1.0000
SYMIG	42	-1616.8855	3483.6981	0.0000	1.0000
SYMI	41	-1621.8760	3487.7283	0.0000	1.0000
HKY	39	-1628.0465	3488.1680	0.0000	1.0000
K2P	36	-1644.7377	3503.6986	0.0000	1.0000
GTR	43	-1624.2801	3504.4377	0.0000	1.0000
SYM	40	-1643.0058	3524.0372	0.0000	1.0000
F81G	39	-1648.8781	3529.8313	0.0000	1.0000
F81IG	40	-1648.8473	3535.7202	0.0000	1.0000
JC69G	36	-1661.4812	3537.1855	0.0000	1.0000
F81I	39	-1652.5812	3537.2374	0.0000	1.0000
JC69IG	37	-1661.4317	3543.0372	0.0000	1.0000
JC69I	36	-1665.1120	3544.4471	0.0000	1.0000
F81	38	-1673.6329	3573.3902	0.0000	1.0000
JC69	35	-1685.8038	3579.8800	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/chr8_4319.phylip = 1 - 384;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4319.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/chr8_4319.phylip = 1 - 384;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4319.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/chr8_4319.phylip = 1 - 384;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4319.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

