
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:31 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/chr9_3633.phylip" (19 taxa, 1097 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	-5262.9555	10617.6752	0.9992	0.9992
GTRIG	45	-5269.2046	10632.3483	0.0007	0.9999
HKYG	40	-5276.5689	10636.2438	0.0001	1.0000
HKYIG	41	-5276.4567	10638.1779	0.0000	1.0000
GTRI	44	-5285.7260	10663.2162	0.0000	1.0000
HKYI	40	-5297.6977	10678.5015	0.0000	1.0000
K2PG	37	-5322.7015	10722.0584	0.0000	1.0000
SYMG	41	-5319.9906	10725.2456	0.0000	1.0000
SYMIG	42	-5319.9050	10727.2369	0.0000	1.0000
K2PIG	38	-5329.7645	10738.3305	0.0000	1.0000
SYMI	41	-5339.4899	10764.2442	0.0000	1.0000
K2PI	37	-5350.9689	10778.5931	0.0000	1.0000
GTR	43	-5395.9397	10881.4728	0.0000	1.0000
HKY	39	-5409.8453	10900.6423	0.0000	1.0000
F81G	39	-5430.5502	10942.0521	0.0000	1.0000
F81IG	40	-5430.4882	10944.0825	0.0000	1.0000
F81I	39	-5448.2704	10977.4927	0.0000	1.0000
K2P	36	-5460.9240	10996.3612	0.0000	1.0000
SYM	40	-5457.1332	10997.3726	0.0000	1.0000
JC69G	36	-5462.9403	11000.3938	0.0000	1.0000
JC69IG	37	-5462.8880	11002.4313	0.0000	1.0000
JC69I	36	-5480.6558	11035.8248	0.0000	1.0000
F81	38	-5554.9607	11188.7229	0.0000	1.0000
JC69	35	-5590.4892	11253.3535	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-5262.9555	10613.9109	0.9992	0.9992
GTRIG	45	-5269.2046	10628.4092	0.0007	0.9999
HKYG	40	-5276.5689	10633.1378	0.0001	1.0000
HKYIG	41	-5276.4567	10634.9134	0.0000	1.0000
GTRI	44	-5285.7260	10659.4519	0.0000	1.0000
HKYI	40	-5297.6977	10675.3954	0.0000	1.0000
K2PG	37	-5322.7015	10719.4030	0.0000	1.0000
SYMG	41	-5319.9906	10721.9811	0.0000	1.0000
SYMIG	42	-5319.9050	10723.8099	0.0000	1.0000
K2PIG	38	-5329.7645	10735.5290	0.0000	1.0000
SYMI	41	-5339.4899	10760.9798	0.0000	1.0000
K2PI	37	-5350.9689	10775.9378	0.0000	1.0000
GTR	43	-5395.9397	10877.8793	0.0000	1.0000
HKY	39	-5409.8453	10897.6906	0.0000	1.0000
F81G	39	-5430.5502	10939.1004	0.0000	1.0000
F81IG	40	-5430.4882	10940.9765	0.0000	1.0000
F81I	39	-5448.2704	10974.5409	0.0000	1.0000
K2P	36	-5460.9240	10993.8480	0.0000	1.0000
SYM	40	-5457.1332	10994.2665	0.0000	1.0000
JC69G	36	-5462.9403	10997.8806	0.0000	1.0000
JC69IG	37	-5462.8880	10999.7759	0.0000	1.0000
JC69I	36	-5480.6558	11033.3116	0.0000	1.0000
F81	38	-5554.9607	11185.9214	0.0000	1.0000
JC69	35	-5590.4892	11250.9784	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-5276.5689	10833.1511	0.5839	0.5839
GTRG	44	-5262.9555	10833.9256	0.3964	0.9803
HKYIG	41	-5276.4567	10839.9271	0.0197	1.0000
GTRIG	45	-5269.2046	10853.4243	0.0000	1.0000
HKYI	40	-5297.6977	10875.4088	0.0000	1.0000
GTRI	44	-5285.7260	10879.4667	0.0000	1.0000
K2PG	37	-5322.7015	10904.4154	0.0000	1.0000
K2PIG	38	-5329.7645	10925.5417	0.0000	1.0000
SYMG	41	-5319.9906	10926.9948	0.0000	1.0000
SYMIG	42	-5319.9050	10933.8240	0.0000	1.0000
K2PI	37	-5350.9689	10960.9502	0.0000	1.0000
SYMI	41	-5339.4899	10965.9935	0.0000	1.0000
HKY	39	-5409.8453	11092.7036	0.0000	1.0000
GTR	43	-5395.9397	11092.8937	0.0000	1.0000
F81G	39	-5430.5502	11134.1134	0.0000	1.0000
F81IG	40	-5430.4882	11140.9899	0.0000	1.0000
F81I	39	-5448.2704	11169.5539	0.0000	1.0000
K2P	36	-5460.9240	11173.8600	0.0000	1.0000
JC69G	36	-5462.9403	11177.8926	0.0000	1.0000
JC69IG	37	-5462.8880	11184.7883	0.0000	1.0000
SYM	40	-5457.1332	11194.2799	0.0000	1.0000
JC69I	36	-5480.6558	11213.3237	0.0000	1.0000
F81	38	-5554.9607	11375.9341	0.0000	1.0000
JC69	35	-5590.4892	11425.9901	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/chr9_3633.phylip = 1 - 1097;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_3633.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/chr9_3633.phylip = 1 - 1097;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_3633.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/chr9_3633.phylip = 1 - 1097;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_3633.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

