
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:30 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/chr6_3252.phylip" (19 taxa, 876 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	-2918.8298	5930.4250	0.6916	0.6916
GTRIG	45	-2918.5454	5932.0788	0.3025	0.9941
GTRI	44	-2923.6228	5940.0110	0.0057	0.9999
HKYG	40	-2932.2692	5948.4665	0.0001	1.0000
HKYIG	41	-2931.8896	5949.9086	0.0000	1.0000
HKYI	40	-2936.8073	5957.5427	0.0000	1.0000
SYMG	41	-2952.3799	5990.8893	0.0000	1.0000
SYMIG	42	-2951.9543	5992.2447	0.0000	1.0000
SYMI	41	-2957.0305	6000.1904	0.0000	1.0000
K2PG	37	-2963.3544	6004.0643	0.0000	1.0000
K2PIG	38	-2962.8706	6005.2824	0.0000	1.0000
GTR	43	-2960.4509	6011.4499	0.0000	1.0000
K2PI	37	-2967.8777	6013.1110	0.0000	1.0000
HKY	39	-2975.6985	6033.1290	0.0000	1.0000
SYM	40	-2998.1625	6080.2531	0.0000	1.0000
F81G	39	-3004.6183	6090.9687	0.0000	1.0000
F81IG	40	-3004.2754	6092.4789	0.0000	1.0000
K2P	36	-3009.9643	6095.1039	0.0000	1.0000
F81I	39	-3008.9345	6099.6011	0.0000	1.0000
JC69G	36	-3031.3004	6137.7760	0.0000	1.0000
JC69IG	37	-3030.9064	6139.1683	0.0000	1.0000
JC69I	36	-3035.6230	6146.4212	0.0000	1.0000
F81	38	-3047.3015	6174.1442	0.0000	1.0000
JC69	35	-3075.6798	6224.3595	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2918.8298	5925.6597	0.6679	0.6679
GTRIG	45	-2918.5454	5927.0908	0.3265	0.9944
GTRI	44	-2923.6228	5935.2456	0.0055	0.9999
HKYG	40	-2932.2692	5944.5383	0.0001	1.0000
HKYIG	41	-2931.8896	5945.7791	0.0000	1.0000
HKYI	40	-2936.8073	5953.6145	0.0000	1.0000
SYMG	41	-2952.3799	5986.7598	0.0000	1.0000
SYMIG	42	-2951.9543	5987.9086	0.0000	1.0000
SYMI	41	-2957.0305	5996.0609	0.0000	1.0000
K2PG	37	-2963.3544	6000.7087	0.0000	1.0000
K2PIG	38	-2962.8706	6001.7412	0.0000	1.0000
GTR	43	-2960.4509	6006.9018	0.0000	1.0000
K2PI	37	-2967.8777	6009.7554	0.0000	1.0000
HKY	39	-2975.6985	6029.3970	0.0000	1.0000
SYM	40	-2998.1625	6076.3249	0.0000	1.0000
F81G	39	-3004.6183	6087.2366	0.0000	1.0000
F81IG	40	-3004.2754	6088.5508	0.0000	1.0000
K2P	36	-3009.9643	6091.9287	0.0000	1.0000
F81I	39	-3008.9345	6095.8691	0.0000	1.0000
JC69G	36	-3031.3004	6134.6008	0.0000	1.0000
JC69IG	37	-3030.9064	6135.8127	0.0000	1.0000
JC69I	36	-3035.6230	6143.2460	0.0000	1.0000
F81	38	-3047.3015	6170.6030	0.0000	1.0000
JC69	35	-3075.6798	6221.3595	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2932.2692	6135.5530	0.4994	0.4994
GTRG	44	-2918.8298	6135.7758	0.4468	0.9462
HKYIG	41	-2931.8896	6141.5691	0.0247	0.9709
GTRIG	45	-2918.5454	6141.9823	0.0201	0.9910
HKYI	40	-2936.8073	6144.6292	0.0053	0.9963
GTRI	44	-2923.6228	6145.3617	0.0037	1.0000
K2PG	37	-2963.3544	6177.3972	0.0000	1.0000
SYMG	41	-2952.3799	6182.5498	0.0000	1.0000
K2PIG	38	-2962.8706	6183.2051	0.0000	1.0000
K2PI	37	-2967.8777	6186.4439	0.0000	1.0000
SYMIG	42	-2951.9543	6188.4740	0.0000	1.0000
SYMI	41	-2957.0305	6191.8509	0.0000	1.0000
GTR	43	-2960.4509	6212.2426	0.0000	1.0000
HKY	39	-2975.6985	6215.6362	0.0000	1.0000
K2P	36	-3009.9643	6263.8418	0.0000	1.0000
SYM	40	-2998.1625	6267.3396	0.0000	1.0000
F81G	39	-3004.6183	6273.4759	0.0000	1.0000
F81IG	40	-3004.2754	6279.5654	0.0000	1.0000
F81I	39	-3008.9345	6282.1083	0.0000	1.0000
JC69G	36	-3031.3004	6306.5140	0.0000	1.0000
JC69IG	37	-3030.9064	6312.5013	0.0000	1.0000
JC69I	36	-3035.6230	6315.1592	0.0000	1.0000
F81	38	-3047.3015	6352.0669	0.0000	1.0000
JC69	35	-3075.6798	6388.4974	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/chr6_3252.phylip = 1 - 876;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3252.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/chr6_3252.phylip = 1 - 876;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3252.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/chr6_3252.phylip = 1 - 876;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3252.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

