
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:22 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/chr12_1169.phylip" (19 taxa, 700 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
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
HKYIG	41	-2805.3558	5697.9457	0.5562	0.5562
HKYG	40	-2806.9138	5698.8047	0.3620	0.9181
GTRIG	45	-2803.1498	5702.6298	0.0535	0.9716
GTRG	44	-2804.9275	5703.9009	0.0283	0.9999
HKYI	40	-2815.1373	5715.2519	0.0001	1.0000
GTRI	44	-2813.2774	5720.6007	0.0000	1.0000
K2PIG	38	-2826.3357	5733.1555	0.0000	1.0000
K2PG	37	-2827.8025	5733.8528	0.0000	1.0000
SYMIG	42	-2822.2717	5734.0410	0.0000	1.0000
SYMG	41	-2824.0132	5735.2604	0.0000	1.0000
K2PI	37	-2835.6711	5749.5900	0.0000	1.0000
SYMI	41	-2831.9557	5751.1454	0.0000	1.0000
F81IG	40	-2854.2935	5793.5643	0.0000	1.0000
F81G	39	-2855.6199	5793.9671	0.0000	1.0000
F81I	39	-2863.3884	5809.5042	0.0000	1.0000
JC69IG	37	-2871.7128	5821.6733	0.0000	1.0000
JC69G	36	-2872.9270	5821.8721	0.0000	1.0000
JC69I	36	-2880.5386	5837.0953	0.0000	1.0000
HKY	39	-2888.8877	5860.5028	0.0000	1.0000
GTR	43	-2888.3201	5868.4084	0.0000	1.0000
K2P	36	-2909.0321	5894.0822	0.0000	1.0000
SYM	40	-2907.6667	5900.3106	0.0000	1.0000
F81	38	-2934.3976	5949.2793	0.0000	1.0000
JC69	35	-2951.2295	5976.2541	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-2805.3558	5692.7116	0.5509	0.5509
HKYG	40	-2806.9138	5693.8275	0.3153	0.8662
GTRIG	45	-2803.1498	5696.2996	0.0916	0.9578
GTRG	44	-2804.9275	5697.8551	0.0421	0.9999
HKYI	40	-2815.1373	5710.2746	0.0001	1.0000
GTRI	44	-2813.2774	5714.5549	0.0000	1.0000
SYMIG	42	-2822.2717	5728.5433	0.0000	1.0000
K2PIG	38	-2826.3357	5728.6713	0.0000	1.0000
K2PG	37	-2827.8025	5729.6050	0.0000	1.0000
SYMG	41	-2824.0132	5730.0264	0.0000	1.0000
K2PI	37	-2835.6711	5745.3422	0.0000	1.0000
SYMI	41	-2831.9557	5745.9114	0.0000	1.0000
F81IG	40	-2854.2935	5788.5871	0.0000	1.0000
F81G	39	-2855.6199	5789.2398	0.0000	1.0000
F81I	39	-2863.3884	5804.7769	0.0000	1.0000
JC69IG	37	-2871.7128	5817.4256	0.0000	1.0000
JC69G	36	-2872.9270	5817.8540	0.0000	1.0000
JC69I	36	-2880.5386	5833.0772	0.0000	1.0000
HKY	39	-2888.8877	5855.7755	0.0000	1.0000
GTR	43	-2888.3201	5862.6401	0.0000	1.0000
K2P	36	-2909.0321	5890.0641	0.0000	1.0000
SYM	40	-2907.6667	5895.3333	0.0000	1.0000
F81	38	-2934.3976	5944.7952	0.0000	1.0000
JC69	35	-2951.2295	5972.4589	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2806.9138	5875.8707	0.8476	0.8476
HKYIG	41	-2805.3558	5879.3059	0.1521	0.9997
HKYI	40	-2815.1373	5892.3178	0.0002	1.0000
K2PG	37	-2827.8025	5897.9950	0.0000	1.0000
GTRG	44	-2804.9275	5898.1026	0.0000	1.0000
GTRIG	45	-2803.1498	5901.0982	0.0000	1.0000
K2PIG	38	-2826.3357	5901.6124	0.0000	1.0000
K2PI	37	-2835.6711	5913.7322	0.0000	1.0000
GTRI	44	-2813.2774	5914.8024	0.0000	1.0000
SYMG	41	-2824.0132	5916.6207	0.0000	1.0000
SYMIG	42	-2822.2717	5919.6887	0.0000	1.0000
SYMI	41	-2831.9557	5932.5057	0.0000	1.0000
F81G	39	-2855.6199	5966.7320	0.0000	1.0000
F81IG	40	-2854.2935	5970.6303	0.0000	1.0000
JC69G	36	-2872.9270	5981.6929	0.0000	1.0000
F81I	39	-2863.3884	5982.2690	0.0000	1.0000
JC69IG	37	-2871.7128	5985.8156	0.0000	1.0000
JC69I	36	-2880.5386	5996.9161	0.0000	1.0000
HKY	39	-2888.8877	6033.2676	0.0000	1.0000
K2P	36	-2909.0321	6053.9030	0.0000	1.0000
GTR	43	-2888.3201	6058.3366	0.0000	1.0000
SYM	40	-2907.6667	6077.3766	0.0000	1.0000
F81	38	-2934.3976	6117.7362	0.0000	1.0000
JC69	35	-2951.2295	6131.7468	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_1169.phylip = 1 - 700;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_1169.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_1169.phylip = 1 - 700;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_1169.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) 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/chr12_1169.phylip = 1 - 700;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_1169.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

