
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:23 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/chr1_29839.phylip" (19 taxa, 483 characters)

Minimum AIC  model: SYMG
Minimum AICc model: SYMG
Minimum BIC  model: SYMG


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
SYMG	41	-2195.9840	4481.7776	0.6524	0.6524
SYMIG	42	-2195.5781	4483.3652	0.2950	0.9474
GTRG	44	-2195.2503	4487.5417	0.0365	0.9839
GTRIG	45	-2194.8855	4489.2446	0.0156	0.9995
SYMI	41	-2203.5017	4496.8130	0.0004	0.9999
K2PG	37	-2210.5998	4501.5188	0.0000	0.9999
GTRI	44	-2202.4573	4501.9558	0.0000	0.9999
HKYG	40	-2207.3719	4502.1646	0.0000	1.0000
K2PIG	38	-2210.0313	4502.7382	0.0000	1.0000
HKYIG	41	-2206.7401	4503.2898	0.0000	1.0000
K2PI	37	-2218.8438	4518.0068	0.0000	1.0000
HKYI	40	-2215.9545	4519.3299	0.0000	1.0000
F81G	39	-2243.1236	4571.2902	0.0000	1.0000
JC69G	36	-2247.3368	4572.6466	0.0000	1.0000
F81IG	40	-2242.6676	4572.7560	0.0000	1.0000
JC69IG	37	-2246.9035	4574.1262	0.0000	1.0000
F81I	39	-2250.9219	4586.8868	0.0000	1.0000
JC69I	36	-2254.9433	4587.8597	0.0000	1.0000
SYM	40	-2263.1849	4613.7906	0.0000	1.0000
GTR	43	-2262.2327	4619.0850	0.0000	1.0000
K2P	36	-2277.9392	4633.8514	0.0000	1.0000
HKY	39	-2274.8693	4634.7815	0.0000	1.0000
JC69	35	-2312.3157	4700.2689	0.0000	1.0000
F81	38	-2308.8326	4700.3408	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
SYMG	41	-2195.9840	4473.9680	0.5843	0.5843
SYMIG	42	-2195.5781	4475.1561	0.3226	0.9069
GTRG	44	-2195.2503	4478.5006	0.0606	0.9675
GTRIG	45	-2194.8855	4479.7709	0.0321	0.9996
SYMI	41	-2203.5017	4489.0035	0.0003	0.9999
GTRI	44	-2202.4573	4492.9147	0.0000	0.9999
HKYG	40	-2207.3719	4494.7438	0.0000	1.0000
K2PG	37	-2210.5998	4495.1997	0.0000	1.0000
HKYIG	41	-2206.7401	4495.4802	0.0000	1.0000
K2PIG	38	-2210.0313	4496.0626	0.0000	1.0000
K2PI	37	-2218.8438	4511.6877	0.0000	1.0000
HKYI	40	-2215.9545	4511.9091	0.0000	1.0000
F81G	39	-2243.1236	4564.2473	0.0000	1.0000
F81IG	40	-2242.6676	4565.3352	0.0000	1.0000
JC69G	36	-2247.3368	4566.6735	0.0000	1.0000
JC69IG	37	-2246.9035	4567.8071	0.0000	1.0000
F81I	39	-2250.9219	4579.8439	0.0000	1.0000
JC69I	36	-2254.9433	4581.8866	0.0000	1.0000
SYM	40	-2263.1849	4606.3698	0.0000	1.0000
GTR	43	-2262.2327	4610.4654	0.0000	1.0000
HKY	39	-2274.8693	4627.7387	0.0000	1.0000
K2P	36	-2277.9392	4627.8783	0.0000	1.0000
F81	38	-2308.8326	4693.6651	0.0000	1.0000
JC69	35	-2312.3157	4694.6314	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
SYMG	41	-2195.9840	4645.3487	0.8456	0.8456
K2PG	37	-2210.5998	4649.8603	0.0886	0.9342
SYMIG	42	-2195.5781	4650.7168	0.0577	0.9920
K2PIG	38	-2210.0313	4654.9032	0.0071	0.9991
SYMI	41	-2203.5017	4660.3841	0.0005	0.9996
HKYG	40	-2207.3719	4661.9444	0.0002	0.9998
GTRG	44	-2195.2503	4662.4213	0.0002	0.9999
K2PI	37	-2218.8438	4666.3483	0.0000	1.0000
HKYIG	41	-2206.7401	4666.8609	0.0000	1.0000
GTRIG	45	-2194.8855	4667.8717	0.0000	1.0000
GTRI	44	-2202.4573	4676.8354	0.0000	1.0000
HKYI	40	-2215.9545	4679.1097	0.0000	1.0000
JC69G	36	-2247.3368	4717.1541	0.0000	1.0000
JC69IG	37	-2246.9035	4722.4677	0.0000	1.0000
F81G	39	-2243.1236	4727.2679	0.0000	1.0000
JC69I	36	-2254.9433	4732.3672	0.0000	1.0000
F81IG	40	-2242.6676	4732.5358	0.0000	1.0000
F81I	39	-2250.9219	4742.8645	0.0000	1.0000
SYM	40	-2263.1849	4773.5704	0.0000	1.0000
K2P	36	-2277.9392	4778.3589	0.0000	1.0000
GTR	43	-2262.2327	4790.2061	0.0000	1.0000
HKY	39	-2274.8693	4790.7593	0.0000	1.0000
JC69	35	-2312.3157	4840.9319	0.0000	1.0000
F81	38	-2308.8326	4852.5057	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_29839.phylip = 1 - 483;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_29839.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=Fixed(Equal);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_29839.phylip = 1 - 483;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_29839.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=Fixed(Equal);
END;


[Mrbayes block for the best BIC model (SYMG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_29839.phylip = 1 - 483;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_29839.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=Fixed(Equal);
END;


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End of Output

