
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:04 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/chrZ_14460.phylip" (19 taxa, 609 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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
GTRG	44	-2387.7494	4870.5201	0.6459	0.6459
GTRIG	45	-2387.7509	4872.8553	0.2010	0.8469
GTRI	44	-2389.7260	4874.4733	0.0895	0.9363
HKYG	40	-2395.1022	4875.9791	0.0421	0.9785
HKYIG	41	-2395.1035	4878.2810	0.0133	0.9918
HKYI	40	-2396.8992	4879.5730	0.0070	0.9988
SYMG	41	-2398.0648	4884.2037	0.0007	0.9995
SYMIG	42	-2398.0653	4886.5121	0.0002	0.9997
SYMI	41	-2399.6299	4887.3339	0.0001	0.9999
K2PG	37	-2404.5967	4888.1182	0.0001	1.0000
K2PIG	38	-2404.5992	4890.3984	0.0000	1.0000
K2PI	37	-2406.3958	4891.7164	0.0000	1.0000
GTR	43	-2407.4738	4907.6450	0.0000	1.0000
HKY	39	-2413.1453	4909.7740	0.0000	1.0000
SYM	40	-2416.6691	4919.1129	0.0000	1.0000
K2P	36	-2422.1678	4920.9929	0.0000	1.0000
F81G	39	-2445.3018	4974.0869	0.0000	1.0000
F81IG	40	-2445.3016	4976.3779	0.0000	1.0000
F81I	39	-2447.0905	4977.6644	0.0000	1.0000
JC69G	36	-2455.4610	4987.5794	0.0000	1.0000
JC69IG	37	-2455.4608	4989.8463	0.0000	1.0000
JC69I	36	-2457.2243	4991.1060	0.0000	1.0000
F81	38	-2461.9633	5005.1265	0.0000	1.0000
JC69	35	-2471.9014	5018.2006	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2387.7494	4863.4988	0.6408	0.6408
GTRIG	45	-2387.7509	4865.5018	0.2354	0.8761
GTRI	44	-2389.7260	4867.4521	0.0888	0.9649
HKYG	40	-2395.1022	4870.2045	0.0224	0.9873
HKYIG	41	-2395.1035	4872.2069	0.0082	0.9956
HKYI	40	-2396.8992	4873.7984	0.0037	0.9993
SYMG	41	-2398.0648	4878.1296	0.0004	0.9997
SYMIG	42	-2398.0653	4880.1305	0.0002	0.9999
SYMI	41	-2399.6299	4881.2598	0.0001	0.9999
K2PG	37	-2404.5967	4883.1935	0.0000	1.0000
K2PIG	38	-2404.5992	4885.1984	0.0000	1.0000
K2PI	37	-2406.3958	4886.7917	0.0000	1.0000
GTR	43	-2407.4738	4900.9476	0.0000	1.0000
HKY	39	-2413.1453	4904.2907	0.0000	1.0000
SYM	40	-2416.6691	4913.3383	0.0000	1.0000
K2P	36	-2422.1678	4916.3356	0.0000	1.0000
F81G	39	-2445.3018	4968.6036	0.0000	1.0000
F81IG	40	-2445.3016	4970.6033	0.0000	1.0000
F81I	39	-2447.0905	4972.1811	0.0000	1.0000
JC69G	36	-2455.4610	4982.9220	0.0000	1.0000
JC69IG	37	-2455.4608	4984.9216	0.0000	1.0000
JC69I	36	-2457.2243	4986.4487	0.0000	1.0000
F81	38	-2461.9633	4999.9265	0.0000	1.0000
JC69	35	-2471.9014	5013.8027	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2404.5967	5046.4307	0.4388	0.4388
HKYG	40	-2395.1022	5046.6772	0.3879	0.8267
K2PI	37	-2406.3958	5050.0290	0.0726	0.8993
HKYI	40	-2396.8992	5050.2711	0.0643	0.9636
K2PIG	38	-2404.5992	5052.8475	0.0177	0.9814
HKYIG	41	-2395.1035	5053.0915	0.0157	0.9971
GTRG	44	-2387.7494	5057.6188	0.0016	0.9987
SYMG	41	-2398.0648	5059.0141	0.0008	0.9995
GTRI	44	-2389.7260	5061.5721	0.0002	0.9997
SYMI	41	-2399.6299	5062.1444	0.0002	0.9999
GTRIG	45	-2387.7509	5064.0336	0.0001	1.0000
SYMIG	42	-2398.0653	5065.4269	0.0000	1.0000
K2P	36	-2422.1678	5075.1611	0.0000	1.0000
HKY	39	-2413.1453	5076.3516	0.0000	1.0000
SYM	40	-2416.6691	5089.8110	0.0000	1.0000
GTR	43	-2407.4738	5090.6558	0.0000	1.0000
F81G	39	-2445.3018	5140.6645	0.0000	1.0000
JC69G	36	-2455.4610	5141.7475	0.0000	1.0000
F81I	39	-2447.0905	5144.2420	0.0000	1.0000
JC69I	36	-2457.2243	5145.2742	0.0000	1.0000
F81IG	40	-2445.3016	5147.0760	0.0000	1.0000
JC69IG	37	-2455.4608	5148.1588	0.0000	1.0000
F81	38	-2461.9633	5167.5756	0.0000	1.0000
JC69	35	-2471.9014	5168.2164	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_14460.phylip = 1 - 609;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_14460.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=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_14460.phylip = 1 - 609;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_14460.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=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_14460.phylip = 1 - 609;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_14460.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

