
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:08 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/chr19_362.phylip" (19 taxa, 822 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	-1943.7089	3980.5143	0.4780	0.4780
GTRG	44	-1944.0725	3981.2415	0.3323	0.8103
GTRIG	45	-1943.5550	3982.4451	0.1820	0.9924
HKYI	40	-1953.1997	3990.5991	0.0031	0.9955
HKYG	40	-1953.2801	3990.7598	0.0028	0.9983
HKYIG	41	-1952.6973	3991.8099	0.0017	1.0000
SYMG	41	-1965.4982	4017.4117	0.0000	1.0000
K2PI	37	-1970.3851	4018.3570	0.0000	1.0000
K2PG	37	-1970.4338	4018.4544	0.0000	1.0000
SYMI	41	-1966.0372	4018.4899	0.0000	1.0000
K2PIG	38	-1969.6198	4019.0249	0.0000	1.0000
SYMIG	42	-1967.6548	4023.9463	0.0000	1.0000
GTR	43	-1976.1416	4043.1470	0.0000	1.0000
F81IG	40	-1980.7408	4045.6813	0.0000	1.0000
F81G	39	-1981.9549	4045.8995	0.0000	1.0000
F81I	39	-1981.9555	4045.9007	0.0000	1.0000
HKY	39	-1986.4022	4054.7942	0.0000	1.0000
JC69G	36	-1997.5438	4070.4812	0.0000	1.0000
JC69I	36	-1997.5522	4070.4981	0.0000	1.0000
SYM	40	-1995.8701	4075.9400	0.0000	1.0000
JC69IG	37	-2000.2379	4078.0626	0.0000	1.0000
K2P	36	-2002.9998	4081.3932	0.0000	1.0000
F81	38	-2011.5728	4102.9310	0.0000	1.0000
JC69	35	-2027.1919	4127.5899	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1943.7089	3975.4178	0.4685	0.4685
GTRG	44	-1944.0725	3976.1450	0.3257	0.7941
GTRIG	45	-1943.5550	3977.1101	0.2010	0.9951
HKYI	40	-1953.1997	3986.3993	0.0019	0.9970
HKYG	40	-1953.2801	3986.5601	0.0018	0.9988
HKYIG	41	-1952.6973	3987.3946	0.0012	1.0000
SYMG	41	-1965.4982	4012.9964	0.0000	1.0000
SYMI	41	-1966.0372	4014.0745	0.0000	1.0000
K2PI	37	-1970.3851	4014.7702	0.0000	1.0000
K2PG	37	-1970.4338	4014.8677	0.0000	1.0000
K2PIG	38	-1969.6198	4015.2395	0.0000	1.0000
SYMIG	42	-1967.6548	4019.3096	0.0000	1.0000
GTR	43	-1976.1416	4038.2832	0.0000	1.0000
F81IG	40	-1980.7408	4041.4816	0.0000	1.0000
F81G	39	-1981.9549	4041.9097	0.0000	1.0000
F81I	39	-1981.9555	4041.9109	0.0000	1.0000
HKY	39	-1986.4022	4050.8044	0.0000	1.0000
JC69G	36	-1997.5438	4067.0875	0.0000	1.0000
JC69I	36	-1997.5522	4067.1044	0.0000	1.0000
SYM	40	-1995.8701	4071.7403	0.0000	1.0000
JC69IG	37	-2000.2379	4074.4759	0.0000	1.0000
K2P	36	-2002.9998	4077.9995	0.0000	1.0000
F81	38	-2011.5728	4099.1455	0.0000	1.0000
JC69	35	-2027.1919	4124.3838	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1953.1997	4174.8690	0.4960	0.4960
HKYG	40	-1953.2801	4175.0297	0.4577	0.9537
HKYIG	41	-1952.6973	4180.5759	0.0286	0.9823
GTRI	44	-1943.7089	4182.7344	0.0097	0.9920
GTRG	44	-1944.0725	4183.4616	0.0068	0.9988
K2PI	37	-1970.3851	4189.1046	0.0004	0.9992
GTRIG	45	-1943.5550	4189.1384	0.0004	0.9996
K2PG	37	-1970.4338	4189.2021	0.0004	1.0000
K2PIG	38	-1969.6198	4194.2856	0.0000	1.0000
SYMG	41	-1965.4982	4206.1777	0.0000	1.0000
SYMI	41	-1966.0372	4207.2558	0.0000	1.0000
SYMIG	42	-1967.6548	4217.2027	0.0000	1.0000
F81G	39	-1981.9549	4225.6676	0.0000	1.0000
F81I	39	-1981.9555	4225.6688	0.0000	1.0000
F81IG	40	-1980.7408	4229.9512	0.0000	1.0000
HKY	39	-1986.4022	4234.5623	0.0000	1.0000
JC69G	36	-1997.5438	4236.7102	0.0000	1.0000
JC69I	36	-1997.5522	4236.7271	0.0000	1.0000
GTR	43	-1976.1416	4240.8880	0.0000	1.0000
K2P	36	-2002.9998	4247.6222	0.0000	1.0000
JC69IG	37	-2000.2379	4248.8103	0.0000	1.0000
SYM	40	-1995.8701	4260.2099	0.0000	1.0000
F81	38	-2011.5728	4278.1917	0.0000	1.0000
JC69	35	-2027.1919	4289.2947	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/chr19_362.phylip = 1 - 822;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_362.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/chr19_362.phylip = 1 - 822;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_362.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/chr19_362.phylip = 1 - 822;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_362.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

