
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:43 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_3310.phylip" (19 taxa, 1060 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: GTRIG


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	-4109.3918	8312.8665	0.9995	0.9995
GTRG	44	-4118.6718	8329.2450	0.0003	0.9998
GTRI	44	-4118.8903	8329.6821	0.0002	1.0000
HKYIG	41	-4133.4208	8352.2247	0.0000	1.0000
HKYI	40	-4139.8518	8362.9225	0.0000	1.0000
HKYG	40	-4141.6995	8366.6178	0.0000	1.0000
SYMG	41	-4152.0334	8389.4499	0.0000	1.0000
SYMIG	42	-4151.8418	8391.2352	0.0000	1.0000
K2PG	37	-4162.3429	8401.4373	0.0000	1.0000
SYMI	41	-4158.2935	8401.9701	0.0000	1.0000
K2PIG	38	-4161.9981	8402.8992	0.0000	1.0000
K2PI	37	-4168.6985	8414.1485	0.0000	1.0000
GTR	43	-4218.4824	8526.6892	0.0000	1.0000
F81G	39	-4241.3572	8563.7733	0.0000	1.0000
F81IG	40	-4241.3107	8565.8403	0.0000	1.0000
HKY	39	-4242.9241	8566.9071	0.0000	1.0000
F81I	39	-4248.7306	8578.5200	0.0000	1.0000
JC69G	36	-4263.9033	8602.4107	0.0000	1.0000
SYM	40	-4262.7021	8608.6231	0.0000	1.0000
JC69IG	37	-4267.0884	8610.9282	0.0000	1.0000
JC69I	36	-4270.1135	8614.8310	0.0000	1.0000
K2P	36	-4275.6893	8625.9828	0.0000	1.0000
F81	38	-4334.8749	8748.6528	0.0000	1.0000
JC69	35	-4358.4782	8789.4173	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-4109.3918	8308.7836	0.9995	0.9995
GTRG	44	-4118.6718	8325.3435	0.0003	0.9998
GTRI	44	-4118.8903	8325.7807	0.0002	1.0000
HKYIG	41	-4133.4208	8348.8416	0.0000	1.0000
HKYI	40	-4139.8518	8359.7037	0.0000	1.0000
HKYG	40	-4141.6995	8363.3989	0.0000	1.0000
SYMG	41	-4152.0334	8386.0668	0.0000	1.0000
SYMIG	42	-4151.8418	8387.6836	0.0000	1.0000
SYMI	41	-4158.2935	8398.5870	0.0000	1.0000
K2PG	37	-4162.3429	8398.6858	0.0000	1.0000
K2PIG	38	-4161.9981	8399.9962	0.0000	1.0000
K2PI	37	-4168.6985	8411.3971	0.0000	1.0000
GTR	43	-4218.4824	8522.9648	0.0000	1.0000
F81G	39	-4241.3572	8560.7145	0.0000	1.0000
F81IG	40	-4241.3107	8562.6215	0.0000	1.0000
HKY	39	-4242.9241	8563.8483	0.0000	1.0000
F81I	39	-4248.7306	8575.4611	0.0000	1.0000
JC69G	36	-4263.9033	8599.8066	0.0000	1.0000
SYM	40	-4262.7021	8605.4042	0.0000	1.0000
JC69IG	37	-4267.0884	8608.1768	0.0000	1.0000
JC69I	36	-4270.1135	8612.2269	0.0000	1.0000
K2P	36	-4275.6893	8623.3787	0.0000	1.0000
F81	38	-4334.8749	8745.7497	0.0000	1.0000
JC69	35	-4358.4782	8786.9564	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRIG	45	-4109.3918	8532.2547	0.9945	0.9945
GTRG	44	-4118.6718	8543.8486	0.0030	0.9975
GTRI	44	-4118.8903	8544.2857	0.0024	1.0000
HKYIG	41	-4133.4208	8552.4486	0.0000	1.0000
HKYI	40	-4139.8518	8558.3446	0.0000	1.0000
HKYG	40	-4141.6995	8562.0399	0.0000	1.0000
K2PG	37	-4162.3429	8582.4287	0.0000	1.0000
K2PIG	38	-4161.9981	8588.7051	0.0000	1.0000
SYMG	41	-4152.0334	8589.6738	0.0000	1.0000
K2PI	37	-4168.6985	8595.1400	0.0000	1.0000
SYMIG	42	-4151.8418	8596.2566	0.0000	1.0000
SYMI	41	-4158.2935	8602.1940	0.0000	1.0000
GTR	43	-4218.4824	8736.5038	0.0000	1.0000
F81G	39	-4241.3572	8754.3894	0.0000	1.0000
HKY	39	-4242.9241	8757.5232	0.0000	1.0000
F81IG	40	-4241.3107	8761.2625	0.0000	1.0000
F81I	39	-4248.7306	8769.1361	0.0000	1.0000
JC69G	36	-4263.9033	8778.5834	0.0000	1.0000
JC69I	36	-4270.1135	8791.0038	0.0000	1.0000
JC69IG	37	-4267.0884	8791.9197	0.0000	1.0000
K2P	36	-4275.6893	8802.1555	0.0000	1.0000
SYM	40	-4262.7021	8804.0452	0.0000	1.0000
F81	38	-4334.8749	8934.4587	0.0000	1.0000
JC69	35	-4358.4782	8960.7672	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/chr5_3310.phylip = 1 - 1060;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3310.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/chr5_3310.phylip = 1 - 1060;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3310.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 (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3310.phylip = 1 - 1060;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3310.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;


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End of Output

