
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:06 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/chr2_14284.phylip" (19 taxa, 318 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	-1381.3972	2865.2999	0.8064	0.8064
GTRIG	45	-1381.5968	2868.4143	0.1699	0.9763
HKYG	40	-1390.5198	2872.8808	0.0182	0.9945
HKYIG	41	-1390.4616	2875.4014	0.0052	0.9997
GTRI	44	-1389.6264	2881.7583	0.0002	0.9999
HKYI	40	-1396.0104	2883.8619	0.0001	1.0000
GTR	43	-1409.4784	2918.7671	0.0000	1.0000
K2PG	37	-1420.1281	2924.2990	0.0000	1.0000
K2PIG	38	-1419.8639	2926.3516	0.0000	1.0000
HKY	39	-1419.2037	2927.6305	0.0000	1.0000
K2PI	37	-1422.3923	2928.8274	0.0000	1.0000
SYMG	41	-1417.8392	2930.1567	0.0000	1.0000
SYMIG	42	-1417.5391	2932.2128	0.0000	1.0000
SYMI	41	-1419.7624	2934.0031	0.0000	1.0000
F81G	39	-1426.6104	2942.4437	0.0000	1.0000
F81IG	40	-1426.5874	2945.0159	0.0000	1.0000
F81I	39	-1429.4510	2948.1250	0.0000	1.0000
JC69I	36	-1448.3573	2978.1950	0.0000	1.0000
K2P	36	-1450.4637	2982.4078	0.0000	1.0000
SYM	40	-1447.2671	2986.3754	0.0000	1.0000
JC69G	36	-1452.9904	2987.4612	0.0000	1.0000
JC69IG	37	-1452.8017	2989.6462	0.0000	1.0000
F81	38	-1451.9557	2990.5350	0.0000	1.0000
JC69	35	-1483.2970	3045.5302	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1381.3972	2850.7944	0.7634	0.7634
GTRIG	45	-1381.5968	2853.1937	0.2300	0.9935
HKYG	40	-1390.5198	2861.0396	0.0046	0.9980
HKYIG	41	-1390.4616	2862.9231	0.0018	0.9998
GTRI	44	-1389.6264	2867.2528	0.0002	1.0000
HKYI	40	-1396.0104	2872.0208	0.0000	1.0000
GTR	43	-1409.4784	2904.9568	0.0000	1.0000
K2PG	37	-1420.1281	2914.2562	0.0000	1.0000
K2PIG	38	-1419.8639	2915.7279	0.0000	1.0000
HKY	39	-1419.2037	2916.4074	0.0000	1.0000
SYMG	41	-1417.8392	2917.6784	0.0000	1.0000
K2PI	37	-1422.3923	2918.7845	0.0000	1.0000
SYMIG	42	-1417.5391	2919.0782	0.0000	1.0000
SYMI	41	-1419.7624	2921.5248	0.0000	1.0000
F81G	39	-1426.6104	2931.2207	0.0000	1.0000
F81IG	40	-1426.5874	2933.1748	0.0000	1.0000
F81I	39	-1429.4510	2936.9020	0.0000	1.0000
JC69I	36	-1448.3573	2968.7146	0.0000	1.0000
K2P	36	-1450.4637	2972.9274	0.0000	1.0000
SYM	40	-1447.2671	2974.5342	0.0000	1.0000
JC69G	36	-1452.9904	2977.9808	0.0000	1.0000
JC69IG	37	-1452.8017	2979.6033	0.0000	1.0000
F81	38	-1451.9557	2979.9113	0.0000	1.0000
JC69	35	-1483.2970	3036.5941	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1390.5198	3011.5217	0.8633	0.8633
GTRG	44	-1381.3972	3016.3246	0.0782	0.9415
HKYIG	41	-1390.4616	3017.1672	0.0513	0.9928
GTRIG	45	-1381.5968	3022.4860	0.0036	0.9964
HKYI	40	-1396.0104	3022.5028	0.0036	1.0000
GTRI	44	-1389.6264	3032.7831	0.0000	1.0000
K2PG	37	-1420.1281	3053.4521	0.0000	1.0000
K2PI	37	-1422.3923	3057.9804	0.0000	1.0000
K2PIG	38	-1419.8639	3058.6859	0.0000	1.0000
HKY	39	-1419.2037	3063.1274	0.0000	1.0000
GTR	43	-1409.4784	3066.7250	0.0000	1.0000
SYMG	41	-1417.8392	3071.9225	0.0000	1.0000
SYMI	41	-1419.7624	3075.7689	0.0000	1.0000
SYMIG	42	-1417.5391	3077.0844	0.0000	1.0000
F81G	39	-1426.6104	3077.9407	0.0000	1.0000
F81I	39	-1429.4510	3083.6220	0.0000	1.0000
F81IG	40	-1426.5874	3083.6568	0.0000	1.0000
JC69I	36	-1448.3573	3104.1484	0.0000	1.0000
K2P	36	-1450.4637	3108.3613	0.0000	1.0000
JC69G	36	-1452.9904	3113.4146	0.0000	1.0000
JC69IG	37	-1452.8017	3118.7992	0.0000	1.0000
F81	38	-1451.9557	3122.8693	0.0000	1.0000
SYM	40	-1447.2671	3125.0163	0.0000	1.0000
JC69	35	-1483.2970	3168.2659	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/chr2_14284.phylip = 1 - 318;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_14284.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/chr2_14284.phylip = 1 - 318;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_14284.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/chr2_14284.phylip = 1 - 318;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_14284.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

