
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:35 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_3265.phylip" (19 taxa, 846 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-2992.3133	6077.5704	0.5723	0.5723
GTRIG	45	-2991.5083	6078.1916	0.4195	0.9917
GTRI	44	-2996.5608	6086.0654	0.0082	0.9999
HKYG	40	-3005.7271	6095.5287	0.0001	1.0000
HKYIG	41	-3006.7980	6099.8796	0.0000	1.0000
SYMG	41	-3007.5932	6101.4701	0.0000	1.0000
SYMIG	42	-3006.8761	6102.2504	0.0000	1.0000
HKYI	40	-3009.7469	6103.5684	0.0000	1.0000
K2PG	37	-3015.0349	6107.5500	0.0000	1.0000
SYMI	41	-3011.1123	6108.5081	0.0000	1.0000
K2PIG	38	-3015.7169	6111.1067	0.0000	1.0000
K2PI	37	-3018.9817	6115.4436	0.0000	1.0000
GTR	43	-3057.4074	6205.5330	0.0000	1.0000
HKY	39	-3076.0787	6234.0283	0.0000	1.0000
SYM	40	-3077.1763	6238.4272	0.0000	1.0000
K2P	36	-3088.7889	6252.8708	0.0000	1.0000
F81G	39	-3128.2745	6338.4199	0.0000	1.0000
F81IG	40	-3127.7775	6339.6295	0.0000	1.0000
F81I	39	-3130.9817	6343.8343	0.0000	1.0000
JC69G	36	-3135.8420	6346.9769	0.0000	1.0000
JC69IG	37	-3135.3419	6348.1641	0.0000	1.0000
JC69I	36	-3138.6212	6352.5353	0.0000	1.0000
F81	38	-3192.8909	6465.4547	0.0000	1.0000
JC69	35	-3202.2865	6477.6841	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2992.3133	6072.6266	0.5443	0.5443
GTRIG	45	-2991.5083	6073.0166	0.4479	0.9922
GTRI	44	-2996.5608	6081.1216	0.0078	0.9999
HKYG	40	-3005.7271	6091.4541	0.0000	1.0000
HKYIG	41	-3006.7980	6095.5960	0.0000	1.0000
SYMG	41	-3007.5932	6097.1865	0.0000	1.0000
SYMIG	42	-3006.8761	6097.7523	0.0000	1.0000
HKYI	40	-3009.7469	6099.4938	0.0000	1.0000
K2PG	37	-3015.0349	6104.0698	0.0000	1.0000
SYMI	41	-3011.1123	6104.2245	0.0000	1.0000
K2PIG	38	-3015.7169	6107.4338	0.0000	1.0000
K2PI	37	-3018.9817	6111.9634	0.0000	1.0000
GTR	43	-3057.4074	6200.8148	0.0000	1.0000
HKY	39	-3076.0787	6230.1573	0.0000	1.0000
SYM	40	-3077.1763	6234.3527	0.0000	1.0000
K2P	36	-3088.7889	6249.5778	0.0000	1.0000
F81G	39	-3128.2745	6334.5489	0.0000	1.0000
F81IG	40	-3127.7775	6335.5549	0.0000	1.0000
F81I	39	-3130.9817	6339.9634	0.0000	1.0000
JC69G	36	-3135.8420	6343.6839	0.0000	1.0000
JC69IG	37	-3135.3419	6344.6839	0.0000	1.0000
JC69I	36	-3138.6212	6349.2423	0.0000	1.0000
F81	38	-3192.8909	6461.7818	0.0000	1.0000
JC69	35	-3202.2865	6474.5730	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-3015.0349	6279.4691	0.5108	0.5108
HKYG	40	-3005.7271	6281.0749	0.2288	0.7396
GTRG	44	-2992.3133	6281.2094	0.2140	0.9536
GTRIG	45	-2991.5083	6286.3400	0.0165	0.9701
K2PI	37	-3018.9817	6287.3626	0.0099	0.9799
K2PIG	38	-3015.7169	6287.5735	0.0089	0.9888
HKYI	40	-3009.7469	6289.1146	0.0041	0.9929
GTRI	44	-2996.5608	6289.7045	0.0031	0.9960
HKYIG	41	-3006.7980	6289.9573	0.0027	0.9987
SYMG	41	-3007.5932	6291.5478	0.0012	0.9999
SYMIG	42	-3006.8761	6296.8541	0.0001	1.0000
SYMI	41	-3011.1123	6298.5858	0.0000	1.0000
GTR	43	-3057.4074	6404.6571	0.0000	1.0000
HKY	39	-3076.0787	6415.0376	0.0000	1.0000
K2P	36	-3088.7889	6420.2365	0.0000	1.0000
SYM	40	-3077.1763	6423.9734	0.0000	1.0000
JC69G	36	-3135.8420	6514.3426	0.0000	1.0000
F81G	39	-3128.2745	6519.4292	0.0000	1.0000
JC69I	36	-3138.6212	6519.9010	0.0000	1.0000
JC69IG	37	-3135.3419	6520.0831	0.0000	1.0000
F81I	39	-3130.9817	6524.8436	0.0000	1.0000
F81IG	40	-3127.7775	6525.1757	0.0000	1.0000
JC69	35	-3202.2865	6640.4912	0.0000	1.0000
F81	38	-3192.8909	6641.9216	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_3265.phylip = 1 - 846;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3265.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_3265.phylip = 1 - 846;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3265.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3265.phylip = 1 - 846;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3265.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

