
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:57 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/chr3_17781.phylip" (19 taxa, 779 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	-3427.9290	6949.2531	0.6481	0.6481
GTRIG	45	-3427.4152	6950.4783	0.3512	0.9993
GTRI	44	-3435.0247	6963.4446	0.0005	0.9999
HKYG	40	-3441.2277	6966.8998	0.0001	1.0000
HKYIG	41	-3440.8854	6968.4438	0.0000	1.0000
HKYI	40	-3447.3454	6979.1352	0.0000	1.0000
K2PG	37	-3459.4128	6996.6205	0.0000	1.0000
SYMG	41	-3455.2348	6997.1425	0.0000	1.0000
K2PIG	38	-3459.1151	6998.2357	0.0000	1.0000
SYMIG	42	-3455.0775	6999.0626	0.0000	1.0000
SYMI	41	-3461.6090	7009.8910	0.0000	1.0000
K2PI	37	-3466.0779	7009.9508	0.0000	1.0000
GTR	43	-3506.7392	7104.6267	0.0000	1.0000
HKY	39	-3524.9335	7132.0889	0.0000	1.0000
F81G	39	-3538.6037	7159.4293	0.0000	1.0000
F81IG	40	-3538.3113	7161.0669	0.0000	1.0000
SYM	40	-3541.7547	7167.9539	0.0000	1.0000
F81I	39	-3544.1968	7170.6155	0.0000	1.0000
K2P	36	-3550.5922	7176.7747	0.0000	1.0000
JC69G	36	-3554.2459	7184.0822	0.0000	1.0000
JC69IG	37	-3553.9670	7185.7289	0.0000	1.0000
JC69I	36	-3560.1793	7195.9488	0.0000	1.0000
F81	38	-3621.7490	7323.5035	0.0000	1.0000
JC69	35	-3640.4642	7354.3200	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3427.9290	6943.8580	0.6188	0.6188
GTRIG	45	-3427.4152	6944.8303	0.3806	0.9994
GTRI	44	-3435.0247	6958.0495	0.0005	0.9999
HKYG	40	-3441.2277	6962.4554	0.0001	1.0000
HKYIG	41	-3440.8854	6963.7708	0.0000	1.0000
HKYI	40	-3447.3454	6974.6907	0.0000	1.0000
SYMG	41	-3455.2348	6992.4695	0.0000	1.0000
K2PG	37	-3459.4128	6992.8256	0.0000	1.0000
SYMIG	42	-3455.0775	6994.1550	0.0000	1.0000
K2PIG	38	-3459.1151	6994.2303	0.0000	1.0000
SYMI	41	-3461.6090	7005.2180	0.0000	1.0000
K2PI	37	-3466.0779	7006.1559	0.0000	1.0000
GTR	43	-3506.7392	7099.4784	0.0000	1.0000
HKY	39	-3524.9335	7127.8670	0.0000	1.0000
F81G	39	-3538.6037	7155.2074	0.0000	1.0000
F81IG	40	-3538.3113	7156.6225	0.0000	1.0000
SYM	40	-3541.7547	7163.5094	0.0000	1.0000
F81I	39	-3544.1968	7166.3936	0.0000	1.0000
K2P	36	-3550.5922	7173.1844	0.0000	1.0000
JC69G	36	-3554.2459	7180.4919	0.0000	1.0000
JC69IG	37	-3553.9670	7181.9340	0.0000	1.0000
JC69I	36	-3560.1793	7192.3585	0.0000	1.0000
F81	38	-3621.7490	7319.4981	0.0000	1.0000
JC69	35	-3640.4642	7350.9283	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3441.2277	7148.7758	0.4772	0.4772
GTRG	44	-3427.9290	7148.8105	0.4690	0.9463
GTRIG	45	-3427.4152	7154.4408	0.0281	0.9743
HKYIG	41	-3440.8854	7154.7493	0.0241	0.9984
HKYI	40	-3447.3454	7161.0112	0.0011	0.9995
GTRI	44	-3435.0247	7163.0019	0.0004	0.9999
K2PG	37	-3459.4128	7165.1720	0.0001	1.0000
K2PIG	38	-3459.1151	7171.2347	0.0000	1.0000
K2PI	37	-3466.0779	7178.5023	0.0000	1.0000
SYMG	41	-3455.2348	7183.4480	0.0000	1.0000
SYMIG	42	-3455.0775	7189.7914	0.0000	1.0000
SYMI	41	-3461.6090	7196.1965	0.0000	1.0000
GTR	43	-3506.7392	7299.7729	0.0000	1.0000
HKY	39	-3524.9335	7309.5294	0.0000	1.0000
F81G	39	-3538.6037	7336.8698	0.0000	1.0000
K2P	36	-3550.5922	7340.8728	0.0000	1.0000
F81IG	40	-3538.3113	7342.9429	0.0000	1.0000
F81I	39	-3544.1968	7348.0561	0.0000	1.0000
JC69G	36	-3554.2459	7348.1803	0.0000	1.0000
SYM	40	-3541.7547	7349.8299	0.0000	1.0000
JC69IG	37	-3553.9670	7354.2804	0.0000	1.0000
JC69I	36	-3560.1793	7360.0469	0.0000	1.0000
F81	38	-3621.7490	7496.5025	0.0000	1.0000
JC69	35	-3640.4642	7513.9587	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/chr3_17781.phylip = 1 - 779;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17781.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/chr3_17781.phylip = 1 - 779;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17781.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/chr3_17781.phylip = 1 - 779;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17781.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

