
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:16 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_11329.phylip" (19 taxa, 638 characters)

Minimum AIC  model: HKYG
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	-1937.7694	3961.0329	0.5529	0.5529
HKY	39	-1939.7012	3962.6198	0.2501	0.8030
GTRG	44	-1935.5812	3965.8404	0.0500	0.8530
HKYI	40	-1940.2108	3965.9158	0.0481	0.9011
GTRI	44	-1935.7424	3966.1627	0.0425	0.9436
HKYIG	41	-1939.7559	3967.2902	0.0242	0.9679
GTRIG	45	-1935.5909	3968.1750	0.0156	0.9834
K2PG	37	-1945.4871	3969.6608	0.0074	0.9908
K2PI	37	-1945.6318	3969.9502	0.0064	0.9972
K2PIG	38	-1945.4973	3971.9428	0.0024	0.9996
SYMG	41	-1944.7640	3977.3065	0.0002	0.9997
SYMI	41	-1944.9112	3977.6009	0.0001	0.9999
GTR	43	-1943.3524	3979.0753	0.0001	0.9999
SYMIG	42	-1944.7744	3979.6194	0.0001	1.0000
K2P	36	-1953.1082	3982.6490	0.0000	1.0000
SYM	40	-1952.4809	3990.4560	0.0000	1.0000
F81G	39	-1964.3516	4011.9207	0.0000	1.0000
F81I	39	-1964.4098	4012.0369	0.0000	1.0000
F81IG	40	-1964.3537	4014.2016	0.0000	1.0000
JC69G	36	-1971.2801	4018.9929	0.0000	1.0000
JC69I	36	-1971.3481	4019.1288	0.0000	1.0000
JC69IG	37	-1971.2839	4021.2545	0.0000	1.0000
F81	38	-1971.1962	4023.3407	0.0000	1.0000
JC69	35	-1978.2391	4030.6643	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1937.7694	3955.5388	0.5224	0.5224
HKY	39	-1939.7012	3957.4024	0.2058	0.7282
GTRG	44	-1935.5812	3959.1625	0.0853	0.8135
GTRI	44	-1935.7424	3959.4848	0.0726	0.8862
HKYI	40	-1940.2108	3960.4217	0.0455	0.9316
GTRIG	45	-1935.5909	3961.1818	0.0311	0.9627
HKYIG	41	-1939.7559	3961.5117	0.0264	0.9891
K2PG	37	-1945.4871	3964.9741	0.0047	0.9938
K2PI	37	-1945.6318	3965.2636	0.0040	0.9978
K2PIG	38	-1945.4973	3966.9946	0.0017	0.9995
SYMG	41	-1944.7640	3971.5280	0.0002	0.9997
SYMI	41	-1944.9112	3971.8224	0.0002	0.9998
GTR	43	-1943.3524	3972.7049	0.0001	0.9999
SYMIG	42	-1944.7744	3973.5489	0.0001	1.0000
K2P	36	-1953.1082	3978.2164	0.0000	1.0000
SYM	40	-1952.4809	3984.9618	0.0000	1.0000
F81G	39	-1964.3516	4006.7033	0.0000	1.0000
F81I	39	-1964.4098	4006.8195	0.0000	1.0000
F81IG	40	-1964.3537	4008.7074	0.0000	1.0000
JC69G	36	-1971.2801	4014.5603	0.0000	1.0000
JC69I	36	-1971.3481	4014.6962	0.0000	1.0000
JC69IG	37	-1971.2839	4016.5679	0.0000	1.0000
F81	38	-1971.1962	4018.3924	0.0000	1.0000
JC69	35	-1978.2391	4026.4782	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1945.4871	4129.9326	0.3876	0.3876
K2PI	37	-1945.6318	4130.2221	0.3354	0.7231
HKY	39	-1939.7012	4131.2776	0.1979	0.9209
HKYG	40	-1937.7694	4133.8723	0.0541	0.9750
K2PIG	38	-1945.4973	4136.4114	0.0152	0.9902
K2P	36	-1953.1082	4138.7166	0.0048	0.9950
HKYI	40	-1940.2108	4138.7552	0.0047	0.9997
HKYIG	41	-1939.7559	4144.3036	0.0003	1.0000
SYMG	41	-1944.7640	4154.3199	0.0000	1.0000
SYMI	41	-1944.9112	4154.6143	0.0000	1.0000
GTRG	44	-1935.5812	4155.3294	0.0000	1.0000
GTRI	44	-1935.7424	4155.6516	0.0000	1.0000
SYMIG	42	-1944.7744	4160.7991	0.0000	1.0000
GTRIG	45	-1935.5909	4161.8070	0.0000	1.0000
SYM	40	-1952.4809	4163.2954	0.0000	1.0000
GTR	43	-1943.3524	4164.4134	0.0000	1.0000
JC69G	36	-1971.2801	4175.0605	0.0000	1.0000
JC69I	36	-1971.3481	4175.1964	0.0000	1.0000
F81G	39	-1964.3516	4180.5785	0.0000	1.0000
F81I	39	-1964.4098	4180.6947	0.0000	1.0000
JC69IG	37	-1971.2839	4181.5264	0.0000	1.0000
JC69	35	-1978.2391	4182.5201	0.0000	1.0000
F81IG	40	-1964.3537	4187.0410	0.0000	1.0000
F81	38	-1971.1962	4187.8093	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11329.phylip = 1 - 638;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11329.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 AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11329.phylip = 1 - 638;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11329.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/chrZ_11329.phylip = 1 - 638;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11329.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

