
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:20 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_11146.phylip" (19 taxa, 450 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-1546.6515	3181.3226	0.5423	0.5423
HKYIG	41	-1546.5382	3183.5177	0.1810	0.7233
GTRG	44	-1543.0852	3183.9481	0.1459	0.8692
HKYI	40	-1548.7429	3185.5053	0.0670	0.9362
GTRIG	45	-1542.9531	3186.1537	0.0484	0.9847
GTRI	44	-1545.3411	3188.4599	0.0153	1.0000
K2PG	37	-1560.4433	3201.7118	0.0000	1.0000
K2PIG	38	-1560.3295	3203.8707	0.0000	1.0000
K2PI	37	-1562.4769	3205.7790	0.0000	1.0000
SYMG	41	-1558.6516	3207.7443	0.0000	1.0000
SYMIG	42	-1558.5343	3209.9432	0.0000	1.0000
SYMI	41	-1560.7093	3211.8597	0.0000	1.0000
HKY	39	-1566.9508	3219.5114	0.0000	1.0000
GTR	43	-1563.5358	3222.3918	0.0000	1.0000
K2P	36	-1580.5088	3239.4679	0.0000	1.0000
SYM	40	-1577.8308	3243.6811	0.0000	1.0000
F81G	39	-1613.5353	3312.6803	0.0000	1.0000
F81IG	40	-1613.4523	3314.9241	0.0000	1.0000
F81I	39	-1615.6695	3316.9487	0.0000	1.0000
JC69G	36	-1623.2749	3325.0001	0.0000	1.0000
JC69IG	37	-1623.1928	3327.2109	0.0000	1.0000
JC69I	36	-1625.4622	3329.3747	0.0000	1.0000
F81	38	-1632.8263	3348.8642	0.0000	1.0000
JC69	35	-1642.3793	3360.8456	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1546.6515	3173.3030	0.3962	0.3962
GTRG	44	-1543.0852	3174.1703	0.2568	0.6531
HKYIG	41	-1546.5382	3175.0765	0.1633	0.8163
GTRIG	45	-1542.9531	3175.9061	0.1078	0.9241
HKYI	40	-1548.7429	3177.4857	0.0489	0.9731
GTRI	44	-1545.3411	3178.6821	0.0269	1.0000
K2PG	37	-1560.4433	3194.8866	0.0000	1.0000
K2PIG	38	-1560.3295	3196.6590	0.0000	1.0000
K2PI	37	-1562.4769	3198.9538	0.0000	1.0000
SYMG	41	-1558.6516	3199.3031	0.0000	1.0000
SYMIG	42	-1558.5343	3201.0685	0.0000	1.0000
SYMI	41	-1560.7093	3203.4185	0.0000	1.0000
HKY	39	-1566.9508	3211.9016	0.0000	1.0000
GTR	43	-1563.5358	3213.0716	0.0000	1.0000
K2P	36	-1580.5088	3233.0175	0.0000	1.0000
SYM	40	-1577.8308	3235.6616	0.0000	1.0000
F81G	39	-1613.5353	3305.0706	0.0000	1.0000
F81IG	40	-1613.4523	3306.9045	0.0000	1.0000
F81I	39	-1615.6695	3309.3389	0.0000	1.0000
JC69G	36	-1623.2749	3318.5498	0.0000	1.0000
JC69IG	37	-1623.1928	3320.3857	0.0000	1.0000
JC69I	36	-1625.4622	3322.9244	0.0000	1.0000
F81	38	-1632.8263	3341.6526	0.0000	1.0000
JC69	35	-1642.3793	3354.7587	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1546.6515	3337.6729	0.8417	0.8417
HKYI	40	-1548.7429	3341.8556	0.1040	0.9457
HKYIG	41	-1546.5382	3343.5556	0.0444	0.9901
K2PG	37	-1560.4433	3346.9287	0.0082	0.9983
K2PI	37	-1562.4769	3350.9959	0.0011	0.9994
K2PIG	38	-1560.3295	3352.8104	0.0004	0.9998
GTRG	44	-1543.0852	3354.9772	0.0001	1.0000
GTRI	44	-1545.3411	3359.4890	0.0000	1.0000
GTRIG	45	-1542.9531	3360.8223	0.0000	1.0000
SYMG	41	-1558.6516	3367.7823	0.0000	1.0000
SYMI	41	-1560.7093	3371.8977	0.0000	1.0000
HKY	39	-1566.9508	3372.1623	0.0000	1.0000
SYMIG	42	-1558.5343	3373.6569	0.0000	1.0000
K2P	36	-1580.5088	3380.9504	0.0000	1.0000
GTR	43	-1563.5358	3389.7692	0.0000	1.0000
SYM	40	-1577.8308	3400.0315	0.0000	1.0000
F81G	39	-1613.5353	3465.3312	0.0000	1.0000
JC69G	36	-1623.2749	3466.4827	0.0000	1.0000
F81I	39	-1615.6695	3469.5996	0.0000	1.0000
JC69I	36	-1625.4622	3470.8573	0.0000	1.0000
F81IG	40	-1613.4523	3471.2744	0.0000	1.0000
JC69IG	37	-1623.1928	3472.4278	0.0000	1.0000
F81	38	-1632.8263	3497.8040	0.0000	1.0000
JC69	35	-1642.3793	3498.5823	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11146.phylip = 1 - 450;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11146.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11146.phylip = 1 - 450;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11146.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;


[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_11146.phylip = 1 - 450;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11146.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

