
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:50 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/chr5_3407.phylip" (19 taxa, 595 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	-2080.2817	4255.7634	0.2963	0.2963
GTRG	44	-2080.4877	4256.1754	0.2411	0.5373
HKYI	40	-2085.4985	4256.9177	0.1663	0.7037
HKYG	40	-2085.6503	4257.2213	0.1429	0.8466
GTRIG	45	-2080.2240	4257.9891	0.0974	0.9440
HKYIG	41	-2085.4467	4259.1212	0.0553	0.9992
GTR	43	-2087.8994	4268.6663	0.0005	0.9997
HKY	39	-2093.0113	4269.6441	0.0003	1.0000
K2PI	37	-2102.7327	4284.5138	0.0000	1.0000
K2PG	37	-2102.7947	4284.6380	0.0000	1.0000
K2PIG	38	-2102.6708	4286.6726	0.0000	1.0000
SYMI	41	-2099.4331	4287.0941	0.0000	1.0000
SYMG	41	-2099.5389	4287.3056	0.0000	1.0000
SYMIG	42	-2099.3774	4289.2984	0.0000	1.0000
K2P	36	-2111.0532	4298.8806	0.0000	1.0000
SYM	40	-2107.7192	4301.3590	0.0000	1.0000
F81I	39	-2124.6120	4332.8457	0.0000	1.0000
F81G	39	-2124.8063	4333.2343	0.0000	1.0000
F81IG	40	-2124.5868	4335.0942	0.0000	1.0000
F81	38	-2131.9787	4345.2883	0.0000	1.0000
JC69I	36	-2139.0219	4354.8181	0.0000	1.0000
JC69G	36	-2139.2031	4355.1803	0.0000	1.0000
JC69IG	37	-2139.0000	4357.0486	0.0000	1.0000
JC69	35	-2146.8020	4368.1121	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-2080.2817	4248.5634	0.3484	0.3484
GTRG	44	-2080.4877	4248.9754	0.2835	0.6318
GTRIG	45	-2080.2240	4250.4481	0.1358	0.7676
HKYI	40	-2085.4985	4250.9971	0.1032	0.8708
HKYG	40	-2085.6503	4251.3007	0.0886	0.9594
HKYIG	41	-2085.4467	4252.8933	0.0400	0.9994
GTR	43	-2087.8994	4261.7988	0.0005	0.9998
HKY	39	-2093.0113	4264.0225	0.0002	1.0000
K2PI	37	-2102.7327	4279.4654	0.0000	1.0000
K2PG	37	-2102.7947	4279.5895	0.0000	1.0000
SYMI	41	-2099.4331	4280.8662	0.0000	1.0000
SYMG	41	-2099.5389	4281.0778	0.0000	1.0000
K2PIG	38	-2102.6708	4281.3417	0.0000	1.0000
SYMIG	42	-2099.3774	4282.7549	0.0000	1.0000
K2P	36	-2111.0532	4294.1064	0.0000	1.0000
SYM	40	-2107.7192	4295.4384	0.0000	1.0000
F81I	39	-2124.6120	4327.2241	0.0000	1.0000
F81G	39	-2124.8063	4327.6127	0.0000	1.0000
F81IG	40	-2124.5868	4329.1736	0.0000	1.0000
F81	38	-2131.9787	4339.9574	0.0000	1.0000
JC69I	36	-2139.0219	4350.0439	0.0000	1.0000
JC69G	36	-2139.2031	4350.4061	0.0000	1.0000
JC69IG	37	-2139.0000	4352.0001	0.0000	1.0000
JC69	35	-2146.8020	4363.6041	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-2085.4985	4426.5396	0.5215	0.5215
HKYG	40	-2085.6503	4426.8431	0.4480	0.9695
HKYIG	41	-2085.4467	4432.8244	0.0225	0.9921
HKY	39	-2093.0113	4435.1764	0.0069	0.9990
GTRI	44	-2080.2817	4441.6601	0.0003	0.9993
K2PI	37	-2102.7327	4441.8421	0.0002	0.9995
K2PG	37	-2102.7947	4441.9663	0.0002	0.9998
GTRG	44	-2080.4877	4442.0721	0.0002	1.0000
GTRIG	45	-2080.2240	4447.9334	0.0000	1.0000
K2PIG	38	-2102.6708	4448.1070	0.0000	1.0000
GTR	43	-2087.8994	4450.5070	0.0000	1.0000
K2P	36	-2111.0532	4452.0947	0.0000	1.0000
SYMI	41	-2099.4331	4460.7972	0.0000	1.0000
SYMG	41	-2099.5389	4461.0088	0.0000	1.0000
SYMIG	42	-2099.3774	4467.0745	0.0000	1.0000
SYM	40	-2107.7192	4470.9809	0.0000	1.0000
F81I	39	-2124.6120	4498.3780	0.0000	1.0000
F81G	39	-2124.8063	4498.7666	0.0000	1.0000
F81IG	40	-2124.5868	4504.7161	0.0000	1.0000
F81	38	-2131.9787	4506.7227	0.0000	1.0000
JC69I	36	-2139.0219	4508.0321	0.0000	1.0000
JC69G	36	-2139.2031	4508.3943	0.0000	1.0000
JC69IG	37	-2139.0000	4514.3769	0.0000	1.0000
JC69	35	-2146.8020	4517.2037	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/chr5_3407.phylip = 1 - 595;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3407.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/chr5_3407.phylip = 1 - 595;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3407.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/chr5_3407.phylip = 1 - 595;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3407.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

