
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:14 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_7440.phylip" (19 taxa, 519 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	-1618.3215	3332.9975	0.5628	0.5628
GTRI	44	-1619.0797	3334.5138	0.2637	0.8265
GTRIG	45	-1618.3375	3335.4277	0.1670	0.9934
HKYG	40	-1628.1449	3343.1517	0.0035	0.9969
HKYI	40	-1628.7079	3344.2778	0.0020	0.9989
HKYIG	41	-1628.1587	3345.5375	0.0011	1.0000
GTR	43	-1636.9333	3367.8330	0.0000	1.0000
F81G	39	-1644.1921	3372.8977	0.0000	1.0000
F81I	39	-1644.7601	3374.0338	0.0000	1.0000
F81IG	40	-1644.2018	3375.2655	0.0000	1.0000
HKY	39	-1646.6447	3377.8030	0.0000	1.0000
F81	38	-1661.1547	3404.4844	0.0000	1.0000
SYMG	41	-1661.7492	3412.7185	0.0000	1.0000
SYMI	41	-1662.7025	3414.6250	0.0000	1.0000
SYMIG	42	-1661.7514	3415.0910	0.0000	1.0000
K2PG	37	-1673.3478	3426.5417	0.0000	1.0000
K2PI	37	-1674.0783	3428.0027	0.0000	1.0000
K2PIG	38	-1673.3496	3428.8742	0.0000	1.0000
SYM	40	-1677.7964	3442.4546	0.0000	1.0000
JC69G	36	-1687.6782	3452.8834	0.0000	1.0000
JC69I	36	-1688.4988	3454.5247	0.0000	1.0000
JC69IG	37	-1687.6797	3455.2056	0.0000	1.0000
K2P	36	-1688.8987	3455.3244	0.0000	1.0000
JC69	35	-1702.7910	3480.7994	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1618.3215	3324.6431	0.5446	0.5446
GTRI	44	-1619.0797	3326.1594	0.2552	0.7997
GTRIG	45	-1618.3375	3326.6750	0.1972	0.9969
HKYG	40	-1628.1449	3336.2898	0.0016	0.9985
HKYI	40	-1628.7079	3337.4158	0.0009	0.9994
HKYIG	41	-1628.1587	3338.3174	0.0006	1.0000
GTR	43	-1636.9333	3359.8667	0.0000	1.0000
F81G	39	-1644.1921	3366.3842	0.0000	1.0000
F81I	39	-1644.7601	3367.5203	0.0000	1.0000
F81IG	40	-1644.2018	3368.4036	0.0000	1.0000
HKY	39	-1646.6447	3371.2894	0.0000	1.0000
F81	38	-1661.1547	3398.3094	0.0000	1.0000
SYMG	41	-1661.7492	3405.4983	0.0000	1.0000
SYMI	41	-1662.7025	3407.4049	0.0000	1.0000
SYMIG	42	-1661.7514	3407.5027	0.0000	1.0000
K2PG	37	-1673.3478	3420.6955	0.0000	1.0000
K2PI	37	-1674.0783	3422.1565	0.0000	1.0000
K2PIG	38	-1673.3496	3422.6992	0.0000	1.0000
SYM	40	-1677.7964	3435.5927	0.0000	1.0000
JC69G	36	-1687.6782	3447.3564	0.0000	1.0000
JC69I	36	-1688.4988	3448.9977	0.0000	1.0000
JC69IG	37	-1687.6797	3449.3594	0.0000	1.0000
K2P	36	-1688.8987	3449.7974	0.0000	1.0000
JC69	35	-1702.7910	3475.5820	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1628.1449	3506.3660	0.5826	0.5826
HKYI	40	-1628.7079	3507.4920	0.3318	0.9144
GTRG	44	-1618.3215	3511.7268	0.0399	0.9543
HKYIG	41	-1628.1587	3512.6455	0.0252	0.9796
GTRI	44	-1619.0797	3513.2431	0.0187	0.9983
GTRIG	45	-1618.3375	3518.0107	0.0017	1.0000
F81G	39	-1644.1921	3532.2084	0.0000	1.0000
F81I	39	-1644.7601	3533.3445	0.0000	1.0000
HKY	39	-1646.6447	3537.1137	0.0000	1.0000
F81IG	40	-1644.2018	3538.4798	0.0000	1.0000
GTR	43	-1636.9333	3542.6985	0.0000	1.0000
F81	38	-1661.1547	3559.8817	0.0000	1.0000
K2PG	37	-1673.3478	3578.0160	0.0000	1.0000
K2PI	37	-1674.0783	3579.4770	0.0000	1.0000
SYMG	41	-1661.7492	3579.8264	0.0000	1.0000
SYMI	41	-1662.7025	3581.7330	0.0000	1.0000
K2PIG	38	-1673.3496	3584.2715	0.0000	1.0000
SYMIG	42	-1661.7514	3586.0827	0.0000	1.0000
JC69G	36	-1687.6782	3600.4249	0.0000	1.0000
JC69I	36	-1688.4988	3602.0662	0.0000	1.0000
K2P	36	-1688.8987	3602.8660	0.0000	1.0000
SYM	40	-1677.7964	3605.6689	0.0000	1.0000
JC69IG	37	-1687.6797	3606.6799	0.0000	1.0000
JC69	35	-1702.7910	3624.3987	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_7440.phylip = 1 - 519;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_7440.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_7440.phylip = 1 - 519;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_7440.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_7440.phylip = 1 - 519;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_7440.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

