
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:14 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_24815.phylip" (19 taxa, 933 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: K2PIG


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	-2505.3346	5105.3367	0.8394	0.8394
HKYIG	41	-2511.4842	5108.8337	0.1461	0.9855
GTRI	44	-2510.8268	5114.1130	0.0104	0.9959
HKYI	40	-2516.8134	5117.3039	0.0021	0.9980
GTRG	44	-2512.7741	5118.0077	0.0015	0.9995
HKYG	40	-2518.7868	5121.2507	0.0003	0.9998
K2PIG	38	-2521.6194	5122.5543	0.0002	1.0000
SYMIG	42	-2518.7314	5125.5211	0.0000	1.0000
K2PI	37	-2526.7428	5130.6275	0.0000	1.0000
SYMI	41	-2524.0488	5133.9629	0.0000	1.0000
K2PG	37	-2529.1027	5135.3473	0.0000	1.0000
SYMG	41	-2526.0402	5137.9458	0.0000	1.0000
F81IG	40	-2565.0186	5213.7143	0.0000	1.0000
F81I	39	-2569.0985	5219.6908	0.0000	1.0000
F81G	39	-2570.7611	5223.0160	0.0000	1.0000
JC69IG	37	-2574.3319	5225.8057	0.0000	1.0000
JC69I	36	-2578.3733	5231.7197	0.0000	1.0000
JC69G	36	-2580.1959	5235.3649	0.0000	1.0000
GTR	43	-2597.1920	5284.6404	0.0000	1.0000
HKY	39	-2607.8654	5297.2246	0.0000	1.0000
SYM	40	-2612.8933	5309.4637	0.0000	1.0000
K2P	36	-2620.0338	5315.0408	0.0000	1.0000
F81	38	-2657.1162	5393.5479	0.0000	1.0000
JC69	35	-2667.6056	5408.0206	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2505.3346	5100.6693	0.8840	0.8840
HKYIG	41	-2511.4842	5104.9684	0.1030	0.9870
GTRI	44	-2510.8268	5109.6535	0.0099	0.9969
GTRG	44	-2512.7741	5113.5483	0.0014	0.9983
HKYI	40	-2516.8134	5113.6268	0.0014	0.9997
HKYG	40	-2518.7868	5117.5736	0.0002	0.9999
K2PIG	38	-2521.6194	5119.2388	0.0001	1.0000
SYMIG	42	-2518.7314	5121.4627	0.0000	1.0000
K2PI	37	-2526.7428	5127.4856	0.0000	1.0000
SYMI	41	-2524.0488	5130.0976	0.0000	1.0000
K2PG	37	-2529.1027	5132.2054	0.0000	1.0000
SYMG	41	-2526.0402	5134.0805	0.0000	1.0000
F81IG	40	-2565.0186	5210.0372	0.0000	1.0000
F81I	39	-2569.0985	5216.1969	0.0000	1.0000
F81G	39	-2570.7611	5219.5222	0.0000	1.0000
JC69IG	37	-2574.3319	5222.6638	0.0000	1.0000
JC69I	36	-2578.3733	5228.7465	0.0000	1.0000
JC69G	36	-2580.1959	5232.3917	0.0000	1.0000
GTR	43	-2597.1920	5280.3839	0.0000	1.0000
HKY	39	-2607.8654	5293.7308	0.0000	1.0000
SYM	40	-2612.8933	5305.7866	0.0000	1.0000
K2P	36	-2620.0338	5312.0676	0.0000	1.0000
F81	38	-2657.1162	5390.2324	0.0000	1.0000
JC69	35	-2667.6056	5405.2112	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PIG	38	-2521.6194	5303.0982	0.4477	0.4477
HKYIG	41	-2511.4842	5303.3430	0.3961	0.8438
K2PI	37	-2526.7428	5306.5066	0.0814	0.9252
HKYI	40	-2516.8134	5307.1630	0.0587	0.9839
HKYG	40	-2518.7868	5311.1098	0.0082	0.9921
K2PG	37	-2529.1027	5311.2264	0.0077	0.9997
GTRIG	45	-2505.3346	5318.3975	0.0002	1.0000
GTRI	44	-2510.8268	5322.5433	0.0000	1.0000
SYMIG	42	-2518.7314	5324.6757	0.0000	1.0000
GTRG	44	-2512.7741	5326.4381	0.0000	1.0000
SYMI	41	-2524.0488	5328.4722	0.0000	1.0000
SYMG	41	-2526.0402	5332.4551	0.0000	1.0000
JC69IG	37	-2574.3319	5401.6848	0.0000	1.0000
JC69I	36	-2578.3733	5402.9291	0.0000	1.0000
F81IG	40	-2565.0186	5403.5734	0.0000	1.0000
F81I	39	-2569.0985	5404.8947	0.0000	1.0000
JC69G	36	-2580.1959	5406.5743	0.0000	1.0000
F81G	39	-2570.7611	5408.2200	0.0000	1.0000
HKY	39	-2607.8654	5482.4286	0.0000	1.0000
K2P	36	-2620.0338	5486.2502	0.0000	1.0000
GTR	43	-2597.1920	5488.4353	0.0000	1.0000
SYM	40	-2612.8933	5499.3228	0.0000	1.0000
F81	38	-2657.1162	5574.0918	0.0000	1.0000
JC69	35	-2667.6056	5574.5554	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/chr2_24815.phylip = 1 - 933;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24815.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/chr2_24815.phylip = 1 - 933;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24815.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 (K2PIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24815.phylip = 1 - 933;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24815.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

