
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:21 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_1282.phylip" (19 taxa, 862 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-2829.4713	5754.0162	0.4935	0.4935
GTRG	44	-2830.7944	5754.4358	0.4001	0.8937
HKYIG	41	-2836.0521	5758.3041	0.0578	0.9515
HKYG	40	-2837.4080	5758.8111	0.0449	0.9964
GTRI	44	-2835.6051	5764.0573	0.0033	0.9997
HKYI	40	-2842.2753	5768.5457	0.0003	1.0000
K2PIG	38	-2859.7671	5799.1357	0.0000	1.0000
K2PG	37	-2861.0889	5799.5904	0.0000	1.0000
SYMIG	42	-2857.2562	5802.9227	0.0000	1.0000
SYMG	41	-2858.5366	5803.2733	0.0000	1.0000
K2PI	37	-2866.0025	5809.4176	0.0000	1.0000
SYMI	41	-2863.3393	5812.8786	0.0000	1.0000
GTR	43	-2888.1832	5866.9923	0.0000	1.0000
HKY	39	-2893.6167	5869.0290	0.0000	1.0000
F81IG	40	-2905.2141	5894.4232	0.0000	1.0000
F81G	39	-2906.4201	5894.6358	0.0000	1.0000
F81I	39	-2911.1590	5904.1137	0.0000	1.0000
K2P	36	-2915.5379	5906.3049	0.0000	1.0000
SYM	40	-2912.7948	5909.5847	0.0000	1.0000
JC69IG	37	-2922.6591	5922.7309	0.0000	1.0000
JC69G	36	-2923.8667	5922.9625	0.0000	1.0000
JC69I	36	-2928.6485	5932.5261	0.0000	1.0000
F81	38	-2959.8237	5999.2489	0.0000	1.0000
JC69	35	-2976.9046	6026.8601	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2829.4713	5748.9427	0.5379	0.5379
GTRG	44	-2830.7944	5749.5888	0.3894	0.9273
HKYIG	41	-2836.0521	5754.1041	0.0407	0.9681
HKYG	40	-2837.4080	5754.8160	0.0285	0.9966
GTRI	44	-2835.6051	5759.2103	0.0032	0.9998
HKYI	40	-2842.2753	5764.5506	0.0002	1.0000
K2PIG	38	-2859.7671	5795.5343	0.0000	1.0000
K2PG	37	-2861.0889	5796.1778	0.0000	1.0000
SYMIG	42	-2857.2562	5798.5124	0.0000	1.0000
SYMG	41	-2858.5366	5799.0733	0.0000	1.0000
K2PI	37	-2866.0025	5806.0049	0.0000	1.0000
SYMI	41	-2863.3393	5808.6786	0.0000	1.0000
GTR	43	-2888.1832	5862.3664	0.0000	1.0000
HKY	39	-2893.6167	5865.2334	0.0000	1.0000
F81IG	40	-2905.2141	5890.4281	0.0000	1.0000
F81G	39	-2906.4201	5890.8402	0.0000	1.0000
F81I	39	-2911.1590	5900.3181	0.0000	1.0000
K2P	36	-2915.5379	5903.0758	0.0000	1.0000
SYM	40	-2912.7948	5905.5896	0.0000	1.0000
JC69IG	37	-2922.6591	5919.3183	0.0000	1.0000
JC69G	36	-2923.8667	5919.7334	0.0000	1.0000
JC69I	36	-2928.6485	5929.2970	0.0000	1.0000
F81	38	-2959.8237	5995.6474	0.0000	1.0000
JC69	35	-2976.9046	6023.8092	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2837.4080	5945.1862	0.8764	0.8764
HKYIG	41	-2836.0521	5949.2336	0.1158	0.9923
HKYI	40	-2842.2753	5954.9208	0.0067	0.9990
GTRG	44	-2830.7944	5958.9960	0.0009	0.9999
GTRIG	45	-2829.4713	5963.1091	0.0001	1.0000
GTRI	44	-2835.6051	5968.6175	0.0000	1.0000
K2PG	37	-2861.0889	5972.2702	0.0000	1.0000
K2PIG	38	-2859.7671	5976.3860	0.0000	1.0000
K2PI	37	-2866.0025	5982.0974	0.0000	1.0000
SYMG	41	-2858.5366	5994.2027	0.0000	1.0000
SYMIG	42	-2857.2562	5998.4011	0.0000	1.0000
SYMI	41	-2863.3393	6003.8081	0.0000	1.0000
HKY	39	-2893.6167	6050.8444	0.0000	1.0000
GTR	43	-2888.1832	6067.0144	0.0000	1.0000
K2P	36	-2915.5379	6074.4090	0.0000	1.0000
F81G	39	-2906.4201	6076.4511	0.0000	1.0000
F81IG	40	-2905.2141	6080.7983	0.0000	1.0000
F81I	39	-2911.1590	6085.9290	0.0000	1.0000
JC69G	36	-2923.8667	6091.0665	0.0000	1.0000
JC69IG	37	-2922.6591	6095.4107	0.0000	1.0000
SYM	40	-2912.7948	6095.9598	0.0000	1.0000
JC69I	36	-2928.6485	6100.6301	0.0000	1.0000
F81	38	-2959.8237	6176.4991	0.0000	1.0000
JC69	35	-2976.9046	6190.3832	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_1282.phylip = 1 - 862;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_1282.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_1282.phylip = 1 - 862;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_1282.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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_1282.phylip = 1 - 862;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_1282.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

