
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:54 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_3418.phylip" (19 taxa, 1107 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	-3769.4501	7630.6290	0.6895	0.6895
GTRIG	45	-3769.3284	7632.5588	0.2627	0.9522
GTRI	44	-3772.1279	7635.9847	0.0474	0.9996
HKYG	40	-3781.2973	7645.6715	0.0004	0.9999
HKYI	40	-3783.6931	7650.4630	0.0000	1.0000
HKYIG	41	-3782.8508	7650.9353	0.0000	1.0000
GTR	43	-3814.5188	7718.5974	0.0000	1.0000
HKY	39	-3826.4009	7733.7258	0.0000	1.0000
K2PG	37	-3856.2113	7789.0531	0.0000	1.0000
SYMG	41	-3852.3466	7789.9270	0.0000	1.0000
K2PIG	38	-3856.0248	7790.8250	0.0000	1.0000
SYMIG	42	-3852.1930	7791.7807	0.0000	1.0000
K2PI	37	-3858.7343	7794.0992	0.0000	1.0000
SYMI	41	-3855.1022	7795.4381	0.0000	1.0000
F81G	39	-3887.5687	7856.0616	0.0000	1.0000
F81IG	40	-3887.4497	7857.9763	0.0000	1.0000
F81I	39	-3889.9702	7860.8645	0.0000	1.0000
SYM	40	-3902.4068	7887.8906	0.0000	1.0000
K2P	36	-3906.9723	7888.4343	0.0000	1.0000
F81	38	-3933.3695	7945.5143	0.0000	1.0000
JC69G	36	-3948.7995	7972.0887	0.0000	1.0000
JC69IG	37	-3948.6412	7973.9128	0.0000	1.0000
JC69I	36	-3951.2717	7977.0331	0.0000	1.0000
JC69	35	-3996.3661	8065.0851	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3769.4501	7626.9001	0.6736	0.6736
GTRIG	45	-3769.3284	7628.6568	0.2798	0.9534
GTRI	44	-3772.1279	7632.2559	0.0463	0.9997
HKYG	40	-3781.2973	7642.5946	0.0003	1.0000
HKYI	40	-3783.6931	7647.3861	0.0000	1.0000
HKYIG	41	-3782.8508	7647.7015	0.0000	1.0000
GTR	43	-3814.5188	7715.0377	0.0000	1.0000
HKY	39	-3826.4009	7730.8017	0.0000	1.0000
K2PG	37	-3856.2113	7786.4226	0.0000	1.0000
SYMG	41	-3852.3466	7786.6932	0.0000	1.0000
K2PIG	38	-3856.0248	7788.0497	0.0000	1.0000
SYMIG	42	-3852.1930	7788.3859	0.0000	1.0000
K2PI	37	-3858.7343	7791.4687	0.0000	1.0000
SYMI	41	-3855.1022	7792.2043	0.0000	1.0000
F81G	39	-3887.5687	7853.1375	0.0000	1.0000
F81IG	40	-3887.4497	7854.8994	0.0000	1.0000
F81I	39	-3889.9702	7857.9405	0.0000	1.0000
SYM	40	-3902.4068	7884.8136	0.0000	1.0000
K2P	36	-3906.9723	7885.9445	0.0000	1.0000
F81	38	-3933.3695	7942.7390	0.0000	1.0000
JC69G	36	-3948.7995	7969.5990	0.0000	1.0000
JC69IG	37	-3948.6412	7971.2823	0.0000	1.0000
JC69I	36	-3951.2717	7974.5434	0.0000	1.0000
JC69	35	-3996.3661	8062.7322	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3781.2973	7842.9710	0.8176	0.8176
GTRG	44	-3769.4501	7847.3141	0.0932	0.9108
HKYI	40	-3783.6931	7847.7625	0.0745	0.9852
GTRI	44	-3772.1279	7852.6699	0.0064	0.9916
HKYIG	41	-3782.8508	7853.0873	0.0052	0.9968
GTRIG	45	-3769.3284	7854.0802	0.0032	1.0000
HKY	39	-3826.4009	7926.1687	0.0000	1.0000
GTR	43	-3814.5188	7930.4422	0.0000	1.0000
K2PG	37	-3856.2113	7971.7708	0.0000	1.0000
K2PI	37	-3858.7343	7976.8168	0.0000	1.0000
K2PIG	38	-3856.0248	7978.4072	0.0000	1.0000
SYMG	41	-3852.3466	7992.0790	0.0000	1.0000
SYMI	41	-3855.1022	7997.5901	0.0000	1.0000
SYMIG	42	-3852.1930	7998.7811	0.0000	1.0000
F81G	39	-3887.5687	8048.5044	0.0000	1.0000
F81I	39	-3889.9702	8053.3074	0.0000	1.0000
F81IG	40	-3887.4497	8055.2758	0.0000	1.0000
K2P	36	-3906.9723	8066.2833	0.0000	1.0000
SYM	40	-3902.4068	8085.1900	0.0000	1.0000
F81	38	-3933.3695	8133.0965	0.0000	1.0000
JC69G	36	-3948.7995	8149.9377	0.0000	1.0000
JC69I	36	-3951.2717	8154.8821	0.0000	1.0000
JC69IG	37	-3948.6412	8156.6305	0.0000	1.0000
JC69	35	-3996.3661	8238.0615	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/chr5_3418.phylip = 1 - 1107;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3418.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/chr5_3418.phylip = 1 - 1107;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3418.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/chr5_3418.phylip = 1 - 1107;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3418.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

