
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:55 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/chr7_10820.phylip" (19 taxa, 465 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
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
GTRI	44	-1540.6883	3178.8052	0.4425	0.4425
GTRG	44	-1541.0234	3179.4754	0.3165	0.7590
GTRIG	45	-1540.6905	3181.2617	0.1296	0.8886
HKYG	40	-1547.7163	3183.1685	0.0499	0.9385
HKYI	40	-1547.7801	3183.2960	0.0469	0.9854
HKYIG	41	-1547.7429	3185.6276	0.0146	1.0000
GTR	43	-1552.9906	3200.9693	0.0000	1.0000
HKY	39	-1560.0110	3205.3632	0.0000	1.0000
K2PG	37	-1579.5423	3239.6702	0.0000	1.0000
K2PI	37	-1579.7698	3240.1250	0.0000	1.0000
K2PIG	38	-1579.5709	3242.0996	0.0000	1.0000
SYMG	41	-1577.7801	3245.7020	0.0000	1.0000
SYMI	41	-1577.9122	3245.9663	0.0000	1.0000
SYMIG	42	-1577.7876	3248.1344	0.0000	1.0000
F81I	39	-1581.7093	3248.7598	0.0000	1.0000
F81G	39	-1581.9361	3249.2134	0.0000	1.0000
F81IG	40	-1581.7111	3251.1580	0.0000	1.0000
K2P	36	-1593.1176	3264.4594	0.0000	1.0000
SYM	40	-1590.7753	3269.2864	0.0000	1.0000
F81	38	-1593.4117	3269.7812	0.0000	1.0000
JC69I	36	-1607.2231	3292.6706	0.0000	1.0000
JC69G	36	-1607.3630	3292.9503	0.0000	1.0000
JC69IG	37	-1607.2196	3295.0246	0.0000	1.0000
JC69	35	-1619.5769	3315.0279	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1540.6883	3169.3766	0.4559	0.4559
GTRG	44	-1541.0234	3170.0469	0.3261	0.7820
GTRIG	45	-1540.6905	3171.3811	0.1673	0.9493
HKYG	40	-1547.7163	3175.4327	0.0221	0.9714
HKYI	40	-1547.7801	3175.5602	0.0207	0.9921
HKYIG	41	-1547.7429	3177.4857	0.0079	1.0000
GTR	43	-1552.9906	3191.9812	0.0000	1.0000
HKY	39	-1560.0110	3198.0220	0.0000	1.0000
K2PG	37	-1579.5423	3233.0847	0.0000	1.0000
K2PI	37	-1579.7698	3233.5395	0.0000	1.0000
K2PIG	38	-1579.5709	3235.1419	0.0000	1.0000
SYMG	41	-1577.7801	3237.5602	0.0000	1.0000
SYMI	41	-1577.9122	3237.8244	0.0000	1.0000
SYMIG	42	-1577.7876	3239.5751	0.0000	1.0000
F81I	39	-1581.7093	3241.4186	0.0000	1.0000
F81G	39	-1581.9361	3241.8723	0.0000	1.0000
F81IG	40	-1581.7111	3243.4222	0.0000	1.0000
K2P	36	-1593.1176	3258.2351	0.0000	1.0000
SYM	40	-1590.7753	3261.5506	0.0000	1.0000
F81	38	-1593.4117	3262.8234	0.0000	1.0000
JC69I	36	-1607.2231	3286.4463	0.0000	1.0000
JC69G	36	-1607.3630	3286.7260	0.0000	1.0000
JC69IG	37	-1607.2196	3288.4391	0.0000	1.0000
JC69	35	-1619.5769	3309.1538	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1547.7163	3341.1142	0.5018	0.5018
HKYI	40	-1547.7801	3341.2417	0.4708	0.9727
HKYIG	41	-1547.7429	3347.3093	0.0227	0.9953
GTRI	44	-1540.6883	3351.6262	0.0026	0.9980
GTRG	44	-1541.0234	3352.2965	0.0019	0.9998
GTRIG	45	-1540.6905	3357.7728	0.0001	1.0000
HKY	39	-1560.0110	3359.5615	0.0000	1.0000
GTR	43	-1552.9906	3370.0888	0.0000	1.0000
K2PG	37	-1579.5423	3386.3401	0.0000	1.0000
K2PI	37	-1579.7698	3386.7949	0.0000	1.0000
K2PIG	38	-1579.5709	3392.5393	0.0000	1.0000
F81I	39	-1581.7093	3402.9581	0.0000	1.0000
F81G	39	-1581.9361	3403.4117	0.0000	1.0000
K2P	36	-1593.1176	3407.3485	0.0000	1.0000
SYMG	41	-1577.7801	3407.3837	0.0000	1.0000
SYMI	41	-1577.9122	3407.6480	0.0000	1.0000
F81IG	40	-1581.7111	3409.1037	0.0000	1.0000
SYMIG	42	-1577.7876	3413.5407	0.0000	1.0000
F81	38	-1593.4117	3420.2208	0.0000	1.0000
SYM	40	-1590.7753	3427.2321	0.0000	1.0000
JC69I	36	-1607.2231	3435.5596	0.0000	1.0000
JC69G	36	-1607.3630	3435.8393	0.0000	1.0000
JC69IG	37	-1607.2196	3441.6945	0.0000	1.0000
JC69	35	-1619.5769	3454.1251	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10820.phylip = 1 - 465;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10820.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10820.phylip = 1 - 465;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10820.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr7_10820.phylip = 1 - 465;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10820.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

