
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:27 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/chr1_30390.phylip" (19 taxa, 682 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYG
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
HKYG	40	-2309.9915	4705.1000	0.3519	0.3519
HKYIG	41	-2308.8881	4705.1575	0.3419	0.6939
GTRG	44	-2306.2718	4706.7602	0.1534	0.8473
GTRIG	45	-2305.1632	4706.8358	0.1477	0.9951
K2PG	37	-2318.5490	4715.4645	0.0020	0.9970
K2PIG	38	-2317.5011	4715.6118	0.0018	0.9989
HKYI	40	-2316.4013	4717.9196	0.0006	0.9995
SYMG	41	-2316.3409	4720.0631	0.0002	0.9997
SYMIG	42	-2315.3012	4720.2550	0.0002	0.9998
GTRI	44	-2313.1141	4720.4449	0.0002	1.0000
K2PI	37	-2324.9860	4728.3384	0.0000	1.0000
SYMI	41	-2322.9235	4733.2284	0.0000	1.0000
HKY	39	-2362.5573	4807.9745	0.0000	1.0000
GTR	43	-2359.4632	4810.8574	0.0000	1.0000
F81G	39	-2364.0174	4810.8947	0.0000	1.0000
F81IG	40	-2363.1224	4811.3619	0.0000	1.0000
K2P	36	-2370.3620	4816.8542	0.0000	1.0000
JC69G	36	-2370.5852	4817.3007	0.0000	1.0000
JC69IG	37	-2369.7071	4817.7807	0.0000	1.0000
SYM	40	-2368.2852	4821.6875	0.0000	1.0000
F81I	39	-2369.8345	4822.5288	0.0000	1.0000
JC69I	36	-2376.5554	4829.2410	0.0000	1.0000
F81	38	-2412.4111	4905.4319	0.0000	1.0000
JC69	35	-2418.5754	4911.0518	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-2308.8881	4699.7762	0.2982	0.2982
HKYG	40	-2309.9915	4699.9830	0.2689	0.5672
GTRIG	45	-2305.1632	4700.3263	0.2265	0.7937
GTRG	44	-2306.2718	4700.5435	0.2032	0.9969
K2PIG	38	-2317.5011	4711.0022	0.0011	0.9979
K2PG	37	-2318.5490	4711.0980	0.0010	0.9990
HKYI	40	-2316.4013	4712.8026	0.0004	0.9994
GTRI	44	-2313.1141	4714.2283	0.0002	0.9996
SYMIG	42	-2315.3012	4714.6024	0.0002	0.9998
SYMG	41	-2316.3409	4714.6819	0.0002	1.0000
K2PI	37	-2324.9860	4723.9720	0.0000	1.0000
SYMI	41	-2322.9235	4727.8471	0.0000	1.0000
HKY	39	-2362.5573	4803.1146	0.0000	1.0000
GTR	43	-2359.4632	4804.9263	0.0000	1.0000
F81G	39	-2364.0174	4806.0349	0.0000	1.0000
F81IG	40	-2363.1224	4806.2449	0.0000	1.0000
K2P	36	-2370.3620	4812.7239	0.0000	1.0000
JC69G	36	-2370.5852	4813.1705	0.0000	1.0000
JC69IG	37	-2369.7071	4813.4142	0.0000	1.0000
SYM	40	-2368.2852	4816.5705	0.0000	1.0000
F81I	39	-2369.8345	4817.6690	0.0000	1.0000
JC69I	36	-2376.5554	4825.1108	0.0000	1.0000
F81	38	-2412.4111	4900.8222	0.0000	1.0000
JC69	35	-2418.5754	4907.1509	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2318.5490	4878.5241	0.6957	0.6957
HKYG	40	-2309.9915	4880.9841	0.2034	0.8991
K2PIG	38	-2317.5011	4882.9533	0.0760	0.9750
HKYIG	41	-2308.8881	4885.3025	0.0235	0.9985
K2PI	37	-2324.9860	4891.3981	0.0011	0.9996
HKYI	40	-2316.4013	4893.8038	0.0003	1.0000
GTRG	44	-2306.2718	4899.6448	0.0000	1.0000
SYMG	41	-2316.3409	4900.2081	0.0000	1.0000
GTRIG	45	-2305.1632	4903.9527	0.0000	1.0000
SYMIG	42	-2315.3012	4904.6536	0.0000	1.0000
GTRI	44	-2313.1141	4913.3296	0.0000	1.0000
SYMI	41	-2322.9235	4913.3733	0.0000	1.0000
K2P	36	-2370.3620	4975.6250	0.0000	1.0000
JC69G	36	-2370.5852	4976.0715	0.0000	1.0000
HKY	39	-2362.5573	4979.5908	0.0000	1.0000
JC69IG	37	-2369.7071	4980.8403	0.0000	1.0000
F81G	39	-2364.0174	4982.5111	0.0000	1.0000
F81IG	40	-2363.1224	4987.2461	0.0000	1.0000
JC69I	36	-2376.5554	4988.0119	0.0000	1.0000
F81I	39	-2369.8345	4994.1452	0.0000	1.0000
SYM	40	-2368.2852	4997.5716	0.0000	1.0000
GTR	43	-2359.4632	4999.5026	0.0000	1.0000
JC69	35	-2418.5754	5065.5269	0.0000	1.0000
F81	38	-2412.4111	5072.7734	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_30390.phylip = 1 - 682;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_30390.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_30390.phylip = 1 - 682;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_30390.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;


[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/chr1_30390.phylip = 1 - 682;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_30390.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;


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

