
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:48 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/chr2_18741.phylip" (19 taxa, 1006 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-5185.5674	10465.4473	0.5634	0.5634
GTRG	44	-5187.2345	10466.5896	0.3182	0.8816
HKYIG	41	-5192.1252	10469.8230	0.0632	0.9448
HKYG	40	-5193.6237	10470.6464	0.0419	0.9867
GTRI	44	-5190.5784	10473.2775	0.0112	0.9979
HKYI	40	-5196.6308	10476.6606	0.0021	1.0000
K2PG	37	-5252.5985	10582.1020	0.0000	1.0000
K2PIG	38	-5251.5912	10582.2476	0.0000	1.0000
SYMG	41	-5250.9126	10587.3978	0.0000	1.0000
SYMIG	42	-5250.1219	10587.9945	0.0000	1.0000
K2PI	37	-5256.7895	10590.4840	0.0000	1.0000
SYMI	41	-5255.6692	10596.9110	0.0000	1.0000
HKY	39	-5285.8122	10652.8543	0.0000	1.0000
GTR	43	-5281.7356	10653.4047	0.0000	1.0000
K2P	36	-5343.0807	10760.9107	0.0000	1.0000
SYM	40	-5341.2685	10765.9359	0.0000	1.0000
F81IG	40	-5372.3084	10828.0157	0.0000	1.0000
F81G	39	-5373.9846	10829.1989	0.0000	1.0000
F81I	39	-5375.4576	10832.1449	0.0000	1.0000
JC69IG	37	-5408.0251	10892.9551	0.0000	1.0000
JC69G	36	-5409.4571	10893.6634	0.0000	1.0000
JC69I	36	-5411.6294	10898.0081	0.0000	1.0000
F81	38	-5456.7246	10992.5144	0.0000	1.0000
JC69	35	-5492.6789	11057.9558	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-5185.5674	10461.1348	0.6031	0.6031
GTRG	44	-5187.2345	10462.4689	0.3095	0.9126
HKYIG	41	-5192.1252	10466.2504	0.0467	0.9593
HKYG	40	-5193.6237	10467.2474	0.0284	0.9877
GTRI	44	-5190.5784	10469.1568	0.0109	0.9986
HKYI	40	-5196.6308	10473.2616	0.0014	1.0000
K2PIG	38	-5251.5912	10579.1825	0.0000	1.0000
K2PG	37	-5252.5985	10579.1970	0.0000	1.0000
SYMG	41	-5250.9126	10583.8251	0.0000	1.0000
SYMIG	42	-5250.1219	10584.2437	0.0000	1.0000
K2PI	37	-5256.7895	10587.5790	0.0000	1.0000
SYMI	41	-5255.6692	10593.3383	0.0000	1.0000
GTR	43	-5281.7356	10649.4712	0.0000	1.0000
HKY	39	-5285.8122	10649.6245	0.0000	1.0000
K2P	36	-5343.0807	10758.1615	0.0000	1.0000
SYM	40	-5341.2685	10762.5369	0.0000	1.0000
F81IG	40	-5372.3084	10824.6167	0.0000	1.0000
F81G	39	-5373.9846	10825.9691	0.0000	1.0000
F81I	39	-5375.4576	10828.9151	0.0000	1.0000
JC69IG	37	-5408.0251	10890.0502	0.0000	1.0000
JC69G	36	-5409.4571	10890.9142	0.0000	1.0000
JC69I	36	-5411.6294	10895.2589	0.0000	1.0000
F81	38	-5456.7246	10989.4492	0.0000	1.0000
JC69	35	-5492.6789	11055.3578	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-5193.6237	10663.7969	0.8395	0.8395
HKYIG	41	-5192.1252	10667.7136	0.1184	0.9579
HKYI	40	-5196.6308	10669.8111	0.0415	0.9994
GTRG	44	-5187.2345	10678.6734	0.0005	0.9999
GTRIG	45	-5185.5674	10682.2530	0.0001	1.0000
GTRI	44	-5190.5784	10685.3612	0.0000	1.0000
K2PG	37	-5252.5985	10761.0053	0.0000	1.0000
K2PIG	38	-5251.5912	10765.9045	0.0000	1.0000
K2PI	37	-5256.7895	10769.3873	0.0000	1.0000
SYMG	41	-5250.9126	10785.2884	0.0000	1.0000
SYMIG	42	-5250.1219	10790.6207	0.0000	1.0000
SYMI	41	-5255.6692	10794.8016	0.0000	1.0000
HKY	39	-5285.8122	10841.2602	0.0000	1.0000
GTR	43	-5281.7356	10860.7619	0.0000	1.0000
K2P	36	-5343.0807	10935.0560	0.0000	1.0000
SYM	40	-5341.2685	10959.0864	0.0000	1.0000
F81G	39	-5373.9846	11017.6049	0.0000	1.0000
F81I	39	-5375.4576	11020.5509	0.0000	1.0000
F81IG	40	-5372.3084	11021.1662	0.0000	1.0000
JC69G	36	-5409.4571	11067.8087	0.0000	1.0000
JC69IG	37	-5408.0251	11071.8584	0.0000	1.0000
JC69I	36	-5411.6294	11072.1534	0.0000	1.0000
F81	38	-5456.7246	11176.1713	0.0000	1.0000
JC69	35	-5492.6789	11227.3386	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_18741.phylip = 1 - 1006;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_18741.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_18741.phylip = 1 - 1006;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_18741.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) 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/chr2_18741.phylip = 1 - 1006;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_18741.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

