
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:22 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_6277.phylip" (19 taxa, 460 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-1421.2174	2930.2630	0.5864	0.5864
HKYIG	41	-1421.0398	2932.3189	0.2098	0.7962
HKYI	40	-1422.7979	2933.4240	0.1207	0.9169
GTRG	44	-1418.8273	2935.1968	0.0498	0.9666
GTRIG	45	-1418.6688	2937.3375	0.0171	0.9837
GTRI	44	-1420.3679	2938.2779	0.0107	0.9944
K2PG	37	-1429.9630	2940.5895	0.0034	0.9977
K2PIG	38	-1429.7593	2942.5590	0.0013	0.9990
K2PI	37	-1431.4146	2943.4928	0.0008	0.9997
SYMG	41	-1428.2344	2946.7080	0.0002	0.9999
SYMIG	42	-1428.0524	2948.7667	0.0001	1.0000
SYMI	41	-1429.6270	2949.4932	0.0000	1.0000
HKY	39	-1436.5991	2958.6268	0.0000	1.0000
GTR	43	-1433.8479	2962.7919	0.0000	1.0000
K2P	36	-1446.1973	2970.6925	0.0000	1.0000
SYM	40	-1444.1082	2976.0445	0.0000	1.0000
F81G	39	-1472.9849	3031.3984	0.0000	1.0000
F81IG	40	-1472.8285	3033.4852	0.0000	1.0000
F81I	39	-1474.3604	3034.1494	0.0000	1.0000
JC69G	36	-1480.2507	3038.7993	0.0000	1.0000
JC69IG	37	-1480.0818	3040.8270	0.0000	1.0000
JC69I	36	-1481.6033	3041.5045	0.0000	1.0000
F81	38	-1488.1798	3059.3999	0.0000	1.0000
JC69	35	-1495.8930	3067.7294	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1421.2174	2922.4348	0.5050	0.5050
HKYIG	41	-1421.0398	2924.0797	0.2219	0.7269
HKYI	40	-1422.7979	2925.5959	0.1040	0.8309
GTRG	44	-1418.8273	2925.6547	0.1010	0.9318
GTRIG	45	-1418.6688	2927.3375	0.0435	0.9754
GTRI	44	-1420.3679	2928.7357	0.0216	0.9970
K2PG	37	-1429.9630	2933.9260	0.0016	0.9986
K2PIG	38	-1429.7593	2935.5186	0.0007	0.9993
K2PI	37	-1431.4146	2936.8293	0.0004	0.9997
SYMG	41	-1428.2344	2938.4687	0.0002	0.9999
SYMIG	42	-1428.0524	2940.1048	0.0001	1.0000
SYMI	41	-1429.6270	2941.2539	0.0000	1.0000
HKY	39	-1436.5991	2951.1982	0.0000	1.0000
GTR	43	-1433.8479	2953.6958	0.0000	1.0000
K2P	36	-1446.1973	2964.3946	0.0000	1.0000
SYM	40	-1444.1082	2968.2164	0.0000	1.0000
F81G	39	-1472.9849	3023.9698	0.0000	1.0000
F81IG	40	-1472.8285	3025.6570	0.0000	1.0000
F81I	39	-1474.3604	3026.7209	0.0000	1.0000
JC69G	36	-1480.2507	3032.5014	0.0000	1.0000
JC69IG	37	-1480.0818	3034.1635	0.0000	1.0000
JC69I	36	-1481.6033	3035.2067	0.0000	1.0000
F81	38	-1488.1798	3052.3595	0.0000	1.0000
JC69	35	-1495.8930	3061.7860	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1429.9630	3086.7814	0.4774	0.4774
HKYG	40	-1421.2174	3087.6839	0.3040	0.7814
K2PI	37	-1431.4146	3089.6846	0.1118	0.8932
HKYI	40	-1422.7979	3090.8449	0.0626	0.9557
K2PIG	38	-1429.7593	3092.5052	0.0273	0.9830
HKYIG	41	-1421.0398	3093.4600	0.0169	1.0000
GTRG	44	-1418.8273	3107.4286	0.0000	1.0000
SYMG	41	-1428.2344	3107.8490	0.0000	1.0000
GTRI	44	-1420.3679	3110.5097	0.0000	1.0000
SYMI	41	-1429.6270	3110.6342	0.0000	1.0000
HKY	39	-1436.5991	3112.3161	0.0000	1.0000
K2P	36	-1446.1973	3113.1188	0.0000	1.0000
GTRIG	45	-1418.6688	3113.2427	0.0000	1.0000
SYMIG	42	-1428.0524	3113.6163	0.0000	1.0000
GTR	43	-1433.8479	3131.3385	0.0000	1.0000
SYM	40	-1444.1082	3133.4654	0.0000	1.0000
JC69G	36	-1480.2507	3181.2256	0.0000	1.0000
JC69I	36	-1481.6033	3183.9308	0.0000	1.0000
F81G	39	-1472.9849	3185.0877	0.0000	1.0000
JC69IG	37	-1480.0818	3187.0189	0.0000	1.0000
F81I	39	-1474.3604	3187.8387	0.0000	1.0000
F81IG	40	-1472.8285	3190.9061	0.0000	1.0000
JC69	35	-1495.8930	3206.3789	0.0000	1.0000
F81	38	-1488.1798	3209.3461	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6277.phylip = 1 - 460;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6277.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;


[Mrbayes block for the best AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6277.phylip = 1 - 460;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6277.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;


[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/chr3_6277.phylip = 1 - 460;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6277.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

