
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:27 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/chr5_11292.phylip" (19 taxa, 900 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	-2594.5740	5283.9957	0.3977	0.3977
HKYIG	41	-2599.2511	5284.5161	0.3066	0.7044
HKYG	40	-2601.1114	5286.0413	0.1430	0.8474
GTRG	44	-2596.9537	5286.5390	0.1115	0.9589
HKYI	40	-2602.9241	5289.6666	0.0233	0.9822
GTRI	44	-2598.7905	5290.2126	0.0178	1.0000
K2PIG	38	-2634.4416	5348.3257	0.0000	1.0000
K2PG	37	-2636.9624	5351.1870	0.0000	1.0000
SYMIG	42	-2632.8897	5353.9941	0.0000	1.0000
K2PI	37	-2638.5758	5354.4139	0.0000	1.0000
SYMG	41	-2635.3925	5356.7990	0.0000	1.0000
SYMI	41	-2637.2171	5360.4482	0.0000	1.0000
HKY	39	-2657.5136	5396.6552	0.0000	1.0000
GTR	43	-2654.7989	5400.0183	0.0000	1.0000
F81IG	40	-2662.5357	5408.8897	0.0000	1.0000
F81G	39	-2664.1943	5410.0165	0.0000	1.0000
F81I	39	-2665.6619	5412.9517	0.0000	1.0000
JC69IG	37	-2690.8077	5458.8775	0.0000	1.0000
K2P	36	-2692.3106	5459.7081	0.0000	1.0000
JC69G	36	-2692.8343	5460.7554	0.0000	1.0000
JC69I	36	-2694.8736	5464.8341	0.0000	1.0000
SYM	40	-2691.1702	5466.1588	0.0000	1.0000
F81	38	-2716.7975	5513.0375	0.0000	1.0000
JC69	35	-2745.9740	5564.8646	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2594.5740	5279.1480	0.4878	0.4878
HKYIG	41	-2599.2511	5280.5021	0.2479	0.7357
GTRG	44	-2596.9537	5281.9075	0.1228	0.8585
HKYG	40	-2601.1114	5282.2229	0.1048	0.9633
GTRI	44	-2598.7905	5285.5810	0.0196	0.9829
HKYI	40	-2602.9241	5285.8482	0.0171	1.0000
K2PIG	38	-2634.4416	5344.8832	0.0000	1.0000
K2PG	37	-2636.9624	5347.9248	0.0000	1.0000
SYMIG	42	-2632.8897	5349.7794	0.0000	1.0000
K2PI	37	-2638.5758	5351.1517	0.0000	1.0000
SYMG	41	-2635.3925	5352.7851	0.0000	1.0000
SYMI	41	-2637.2171	5356.4342	0.0000	1.0000
HKY	39	-2657.5136	5393.0273	0.0000	1.0000
GTR	43	-2654.7989	5395.5978	0.0000	1.0000
F81IG	40	-2662.5357	5405.0713	0.0000	1.0000
F81G	39	-2664.1943	5406.3886	0.0000	1.0000
F81I	39	-2665.6619	5409.3238	0.0000	1.0000
JC69IG	37	-2690.8077	5455.6153	0.0000	1.0000
K2P	36	-2692.3106	5456.6212	0.0000	1.0000
JC69G	36	-2692.8343	5457.6685	0.0000	1.0000
JC69I	36	-2694.8736	5461.7472	0.0000	1.0000
SYM	40	-2691.1702	5462.3404	0.0000	1.0000
F81	38	-2716.7975	5509.5950	0.0000	1.0000
JC69	35	-2745.9740	5561.9480	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2601.1114	5474.3187	0.7259	0.7259
HKYIG	41	-2599.2511	5477.4003	0.1555	0.8814
HKYI	40	-2602.9241	5477.9440	0.1185	0.9999
GTRG	44	-2596.9537	5493.2128	0.0001	1.0000
GTRIG	45	-2594.5740	5495.2557	0.0000	1.0000
GTRI	44	-2598.7905	5496.8864	0.0000	1.0000
K2PG	37	-2636.9624	5525.6134	0.0000	1.0000
K2PIG	38	-2634.4416	5527.3742	0.0000	1.0000
K2PI	37	-2638.5758	5528.8403	0.0000	1.0000
SYMG	41	-2635.3925	5549.6832	0.0000	1.0000
SYMIG	42	-2632.8897	5551.4800	0.0000	1.0000
SYMI	41	-2637.2171	5553.3324	0.0000	1.0000
HKY	39	-2657.5136	5580.3207	0.0000	1.0000
F81G	39	-2664.1943	5593.6820	0.0000	1.0000
F81I	39	-2665.6619	5596.6172	0.0000	1.0000
F81IG	40	-2662.5357	5597.1671	0.0000	1.0000
GTR	43	-2654.7989	5602.1008	0.0000	1.0000
K2P	36	-2692.3106	5629.5074	0.0000	1.0000
JC69G	36	-2692.8343	5630.5548	0.0000	1.0000
JC69IG	37	-2690.8077	5633.3039	0.0000	1.0000
JC69I	36	-2694.8736	5634.6334	0.0000	1.0000
SYM	40	-2691.1702	5654.4362	0.0000	1.0000
F81	38	-2716.7975	5692.0860	0.0000	1.0000
JC69	35	-2745.9740	5730.0318	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/chr5_11292.phylip = 1 - 900;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11292.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/chr5_11292.phylip = 1 - 900;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11292.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/chr5_11292.phylip = 1 - 900;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11292.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

