
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:19 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_5453.phylip" (19 taxa, 667 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
Minimum BIC  model: HKYI


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
GTRI	44	-2251.0439	4596.4544	0.4040	0.4040
GTRG	44	-2251.1112	4596.5890	0.3777	0.7817
GTRIG	45	-2251.2110	4599.0886	0.1082	0.8899
HKYI	40	-2257.4268	4600.0933	0.0655	0.9554
HKYG	40	-2258.0890	4601.4176	0.0338	0.9891
HKYIG	41	-2258.0891	4603.6886	0.0109	1.0000
K2PI	37	-2282.3126	4643.0958	0.0000	1.0000
GTR	43	-2275.5583	4643.1904	0.0000	1.0000
SYMI	41	-2278.0817	4643.6738	0.0000	1.0000
HKY	39	-2280.9617	4644.8995	0.0000	1.0000
K2PG	37	-2283.4958	4645.4621	0.0000	1.0000
SYMG	41	-2279.0026	4645.5157	0.0000	1.0000
SYMIG	42	-2278.0986	4645.9857	0.0000	1.0000
K2PIG	38	-2283.6819	4648.0835	0.0000	1.0000
K2P	36	-2306.5345	4689.2975	0.0000	1.0000
SYM	40	-2302.5381	4690.3157	0.0000	1.0000
F81I	39	-2315.1262	4713.2284	0.0000	1.0000
F81IG	40	-2315.1574	4715.5545	0.0000	1.0000
F81G	39	-2316.4294	4715.8349	0.0000	1.0000
JC69I	36	-2337.6467	4751.5220	0.0000	1.0000
JC69IG	37	-2337.6848	4753.8402	0.0000	1.0000
JC69G	36	-2339.2082	4754.6450	0.0000	1.0000
F81	38	-2337.6840	4756.0878	0.0000	1.0000
JC69	35	-2359.9996	4793.9929	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-2251.0439	4590.0879	0.4160	0.4160
GTRG	44	-2251.1112	4590.2224	0.3890	0.8050
GTRIG	45	-2251.2110	4592.4219	0.1295	0.9345
HKYI	40	-2257.4268	4594.8536	0.0384	0.9729
HKYG	40	-2258.0890	4596.1780	0.0198	0.9927
HKYIG	41	-2258.0891	4598.1782	0.0073	1.0000
GTR	43	-2275.5583	4637.1166	0.0000	1.0000
SYMI	41	-2278.0817	4638.1634	0.0000	1.0000
K2PI	37	-2282.3126	4638.6252	0.0000	1.0000
HKY	39	-2280.9617	4639.9235	0.0000	1.0000
SYMG	41	-2279.0026	4640.0053	0.0000	1.0000
SYMIG	42	-2278.0986	4640.1973	0.0000	1.0000
K2PG	37	-2283.4958	4640.9915	0.0000	1.0000
K2PIG	38	-2283.6819	4643.3638	0.0000	1.0000
K2P	36	-2306.5345	4685.0689	0.0000	1.0000
SYM	40	-2302.5381	4685.0761	0.0000	1.0000
F81I	39	-2315.1262	4708.2523	0.0000	1.0000
F81IG	40	-2315.1574	4710.3149	0.0000	1.0000
F81G	39	-2316.4294	4710.8588	0.0000	1.0000
JC69I	36	-2337.6467	4747.2934	0.0000	1.0000
JC69IG	37	-2337.6848	4749.3696	0.0000	1.0000
JC69G	36	-2339.2082	4750.4164	0.0000	1.0000
F81	38	-2337.6840	4751.3681	0.0000	1.0000
JC69	35	-2359.9996	4789.9993	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-2257.4268	4774.9652	0.6501	0.6501
HKYG	40	-2258.0890	4776.2896	0.3353	0.9853
HKYIG	41	-2258.0891	4782.7926	0.0130	0.9983
GTRI	44	-2251.0439	4788.2106	0.0009	0.9992
GTRG	44	-2251.1112	4788.3452	0.0008	1.0000
GTRIG	45	-2251.2110	4795.0475	0.0000	1.0000
K2PI	37	-2282.3126	4805.2285	0.0000	1.0000
K2PG	37	-2283.4958	4807.5948	0.0000	1.0000
K2PIG	38	-2283.6819	4814.4698	0.0000	1.0000
HKY	39	-2280.9617	4815.5323	0.0000	1.0000
SYMI	41	-2278.0817	4822.7778	0.0000	1.0000
SYMG	41	-2279.0026	4824.6197	0.0000	1.0000
SYMIG	42	-2278.0986	4829.3145	0.0000	1.0000
GTR	43	-2275.5583	4830.7366	0.0000	1.0000
K2P	36	-2306.5345	4847.1694	0.0000	1.0000
SYM	40	-2302.5381	4865.1877	0.0000	1.0000
F81I	39	-2315.1262	4883.8612	0.0000	1.0000
F81G	39	-2316.4294	4886.4676	0.0000	1.0000
F81IG	40	-2315.1574	4890.4265	0.0000	1.0000
JC69I	36	-2337.6467	4909.3938	0.0000	1.0000
JC69G	36	-2339.2082	4912.5168	0.0000	1.0000
JC69IG	37	-2337.6848	4915.9728	0.0000	1.0000
F81	38	-2337.6840	4922.4741	0.0000	1.0000
JC69	35	-2359.9996	4947.5969	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5453.phylip = 1 - 667;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5453.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5453.phylip = 1 - 667;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5453.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5453.phylip = 1 - 667;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5453.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


-------------------------------------------------------------
End of Output

