
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:12 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/chr13_707.phylip" (19 taxa, 708 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: HKYG


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	-3229.7073	6553.3874	0.7570	0.7570
GTRIG	45	-3229.7075	6555.6689	0.2419	0.9990
HKYG	40	-3241.1299	6567.1774	0.0008	0.9997
HKYIG	41	-3241.1300	6569.4311	0.0002	1.0000
GTRI	44	-3239.8477	6573.6682	0.0000	1.0000
HKYI	40	-3248.3680	6581.6536	0.0000	1.0000
GTR	43	-3265.9702	6623.6393	0.0000	1.0000
HKY	39	-3279.2194	6641.1095	0.0000	1.0000
K2PG	37	-3284.9647	6648.1264	0.0000	1.0000
K2PIG	38	-3284.9645	6650.3596	0.0000	1.0000
SYMG	41	-3283.4314	6654.0340	0.0000	1.0000
SYMIG	42	-3283.4313	6656.2942	0.0000	1.0000
K2PI	37	-3291.3261	6660.8493	0.0000	1.0000
SYMI	41	-3290.0326	6667.2364	0.0000	1.0000
K2P	36	-3331.3598	6738.6898	0.0000	1.0000
SYM	40	-3329.5554	6744.0284	0.0000	1.0000
F81G	39	-3339.2170	6761.1047	0.0000	1.0000
F81IG	40	-3339.2183	6763.3542	0.0000	1.0000
F81I	39	-3344.8260	6772.3227	0.0000	1.0000
JC69G	36	-3374.5933	6825.1568	0.0000	1.0000
JC69IG	37	-3374.5933	6827.3835	0.0000	1.0000
F81	38	-3376.6177	6833.6659	0.0000	1.0000
JC69I	36	-3380.0864	6836.1429	0.0000	1.0000
JC69	35	-3415.6378	6905.0255	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3229.7073	6547.4146	0.7306	0.7306
GTRIG	45	-3229.7075	6549.4151	0.2687	0.9994
HKYG	40	-3241.1299	6562.2598	0.0004	0.9998
HKYIG	41	-3241.1300	6564.2599	0.0002	1.0000
GTRI	44	-3239.8477	6567.6954	0.0000	1.0000
HKYI	40	-3248.3680	6576.7361	0.0000	1.0000
GTR	43	-3265.9702	6617.9405	0.0000	1.0000
HKY	39	-3279.2194	6636.4388	0.0000	1.0000
K2PG	37	-3284.9647	6643.9293	0.0000	1.0000
K2PIG	38	-3284.9645	6645.9291	0.0000	1.0000
SYMG	41	-3283.4314	6648.8628	0.0000	1.0000
SYMIG	42	-3283.4313	6650.8627	0.0000	1.0000
K2PI	37	-3291.3261	6656.6523	0.0000	1.0000
SYMI	41	-3290.0326	6662.0652	0.0000	1.0000
K2P	36	-3331.3598	6734.7196	0.0000	1.0000
SYM	40	-3329.5554	6739.1108	0.0000	1.0000
F81G	39	-3339.2170	6756.4341	0.0000	1.0000
F81IG	40	-3339.2183	6758.4367	0.0000	1.0000
F81I	39	-3344.8260	6767.6521	0.0000	1.0000
JC69G	36	-3374.5933	6821.1866	0.0000	1.0000
JC69IG	37	-3374.5933	6823.1865	0.0000	1.0000
F81	38	-3376.6177	6829.2354	0.0000	1.0000
JC69I	36	-3380.0864	6832.1727	0.0000	1.0000
JC69	35	-3415.6378	6901.2755	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3241.1299	6744.7576	0.8147	0.8147
GTRG	44	-3229.7073	6748.1621	0.1485	0.9632
HKYIG	41	-3241.1300	6751.3201	0.0306	0.9938
GTRIG	45	-3229.7075	6754.7251	0.0056	0.9994
HKYI	40	-3248.3680	6759.2338	0.0006	1.0000
GTRI	44	-3239.8477	6768.4429	0.0000	1.0000
K2PG	37	-3284.9647	6812.7398	0.0000	1.0000
GTR	43	-3265.9702	6814.1256	0.0000	1.0000
HKY	39	-3279.2194	6814.3742	0.0000	1.0000
K2PIG	38	-3284.9645	6819.3019	0.0000	1.0000
K2PI	37	-3291.3261	6825.4627	0.0000	1.0000
SYMG	41	-3283.4314	6835.9230	0.0000	1.0000
SYMIG	42	-3283.4313	6842.4853	0.0000	1.0000
SYMI	41	-3290.0326	6849.1254	0.0000	1.0000
K2P	36	-3331.3598	6898.9676	0.0000	1.0000
SYM	40	-3329.5554	6921.6086	0.0000	1.0000
F81G	39	-3339.2170	6934.3694	0.0000	1.0000
F81IG	40	-3339.2183	6940.9344	0.0000	1.0000
F81I	39	-3344.8260	6945.5874	0.0000	1.0000
JC69G	36	-3374.5933	6985.4346	0.0000	1.0000
JC69IG	37	-3374.5933	6991.9970	0.0000	1.0000
JC69I	36	-3380.0864	6996.4207	0.0000	1.0000
F81	38	-3376.6177	7002.6083	0.0000	1.0000
JC69	35	-3415.6378	7060.9611	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/chr13_707.phylip = 1 - 708;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_707.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/chr13_707.phylip = 1 - 708;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_707.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_707.phylip = 1 - 708;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_707.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;


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

