
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:18 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/chr4_8888.phylip" (19 taxa, 613 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	-2909.4601	5913.8920	0.7270	0.7270
GTRIG	45	-2909.4510	5916.2035	0.2289	0.9558
SYMG	41	-2916.9203	5921.8721	0.0134	0.9693
HKYG	40	-2918.3034	5922.3412	0.0106	0.9799
K2PG	37	-2921.8751	5922.6405	0.0092	0.9891
SYMIG	42	-2916.8906	5924.1180	0.0044	0.9935
HKYIG	41	-2918.2818	5924.5952	0.0034	0.9969
K2PIG	38	-2921.8309	5924.8256	0.0031	1.0000
GTRI	44	-2919.8219	5934.6156	0.0000	1.0000
SYMI	41	-2926.9946	5942.0207	0.0000	1.0000
K2PI	37	-2932.1510	5943.1925	0.0000	1.0000
HKYI	40	-2928.9334	5943.6011	0.0000	1.0000
GTR	43	-2976.2944	6045.2392	0.0000	1.0000
HKY	39	-2986.4137	6056.2723	0.0000	1.0000
SYM	40	-2986.3974	6058.5290	0.0000	1.0000
K2P	36	-2991.7270	6060.0789	0.0000	1.0000
JC69G	36	-3014.9326	6106.4901	0.0000	1.0000
F81G	39	-3011.7672	6106.9795	0.0000	1.0000
JC69IG	37	-3014.9039	6108.6982	0.0000	1.0000
F81IG	40	-3011.7174	6109.1691	0.0000	1.0000
JC69I	36	-3023.8112	6124.2475	0.0000	1.0000
F81I	39	-3020.5220	6124.4891	0.0000	1.0000
F81	38	-3074.7303	6230.6244	0.0000	1.0000
JC69	35	-3079.2325	6232.8324	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2909.4601	5906.9201	0.7121	0.7121
GTRIG	45	-2909.4510	5908.9019	0.2644	0.9765
SYMG	41	-2916.9203	5915.8406	0.0082	0.9847
HKYG	40	-2918.3034	5916.6069	0.0056	0.9904
K2PG	37	-2921.8751	5917.7501	0.0032	0.9935
SYMIG	42	-2916.8906	5917.7811	0.0031	0.9966
HKYIG	41	-2918.2818	5918.5637	0.0021	0.9988
K2PIG	38	-2921.8309	5919.6618	0.0012	1.0000
GTRI	44	-2919.8219	5927.6438	0.0000	1.0000
SYMI	41	-2926.9946	5935.9892	0.0000	1.0000
HKYI	40	-2928.9334	5937.8668	0.0000	1.0000
K2PI	37	-2932.1510	5938.3020	0.0000	1.0000
GTR	43	-2976.2944	6038.5889	0.0000	1.0000
HKY	39	-2986.4137	6050.8273	0.0000	1.0000
SYM	40	-2986.3974	6052.7947	0.0000	1.0000
K2P	36	-2991.7270	6055.4539	0.0000	1.0000
F81G	39	-3011.7672	6101.5345	0.0000	1.0000
JC69G	36	-3014.9326	6101.8651	0.0000	1.0000
F81IG	40	-3011.7174	6103.4348	0.0000	1.0000
JC69IG	37	-3014.9039	6103.8078	0.0000	1.0000
F81I	39	-3020.5220	6119.0441	0.0000	1.0000
JC69I	36	-3023.8112	6119.6225	0.0000	1.0000
F81	38	-3074.7303	6225.4606	0.0000	1.0000
JC69	35	-3079.2325	6228.4650	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2921.8751	6081.2296	0.9568	0.9568
K2PIG	38	-2921.8309	6087.5597	0.0404	0.9972
HKYG	40	-2918.3034	6093.3415	0.0022	0.9995
SYMG	41	-2916.9203	6096.9936	0.0004	0.9998
HKYIG	41	-2918.2818	6099.7167	0.0001	0.9999
GTRG	44	-2909.4601	6101.3282	0.0000	1.0000
K2PI	37	-2932.1510	6101.7815	0.0000	1.0000
SYMIG	42	-2916.8906	6103.3525	0.0000	1.0000
GTRIG	45	-2909.4510	6107.7283	0.0000	1.0000
HKYI	40	-2928.9334	6114.6014	0.0000	1.0000
SYMI	41	-2926.9946	6117.1422	0.0000	1.0000
GTRI	44	-2919.8219	6122.0518	0.0000	1.0000
K2P	36	-2991.7270	6214.5150	0.0000	1.0000
HKY	39	-2986.4137	6223.1436	0.0000	1.0000
GTR	43	-2976.2944	6228.5786	0.0000	1.0000
SYM	40	-2986.3974	6229.5293	0.0000	1.0000
JC69G	36	-3014.9326	6260.9263	0.0000	1.0000
JC69IG	37	-3014.9039	6267.2873	0.0000	1.0000
F81G	39	-3011.7672	6273.8507	0.0000	1.0000
JC69I	36	-3023.8112	6278.6836	0.0000	1.0000
F81IG	40	-3011.7174	6280.1694	0.0000	1.0000
F81I	39	-3020.5220	6291.3603	0.0000	1.0000
JC69	35	-3079.2325	6383.1077	0.0000	1.0000
F81	38	-3074.7303	6393.3585	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/chr4_8888.phylip = 1 - 613;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_8888.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/chr4_8888.phylip = 1 - 613;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_8888.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/chr4_8888.phylip = 1 - 613;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_8888.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

