
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:23 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/chr3_14127.phylip" (19 taxa, 333 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	-925.7738	1942.7805	0.3685	0.3685
HKYI	40	-925.8170	1942.8669	0.3529	0.7213
HKYIG	41	-925.4785	1944.7920	0.1348	0.8561
GTRI	44	-922.9455	1947.6409	0.0324	0.8885
GTRG	44	-922.9476	1947.6453	0.0324	0.9209
K2PG	37	-932.1320	1947.7961	0.0300	0.9509
K2PI	37	-932.1487	1947.8297	0.0295	0.9804
K2PIG	38	-931.9180	1949.9176	0.0104	0.9908
GTRIG	45	-922.9474	1950.3198	0.0085	0.9993
SYMG	41	-931.5677	1956.9705	0.0003	0.9996
SYMI	41	-931.5783	1956.9916	0.0003	0.9999
SYMIG	42	-931.4632	1959.3815	0.0001	1.0000
F81G	39	-938.9583	1966.5651	0.0000	1.0000
F81I	39	-938.9953	1966.6390	0.0000	1.0000
F81IG	40	-938.6848	1968.6026	0.0000	1.0000
JC69G	36	-945.9702	1972.9404	0.0000	1.0000
JC69I	36	-945.9993	1972.9987	0.0000	1.0000
JC69IG	37	-945.6278	1974.7878	0.0000	1.0000
HKY	39	-949.5791	1987.8067	0.0000	1.0000
GTR	43	-946.9952	1993.0839	0.0000	1.0000
K2P	36	-956.8367	1994.6734	0.0000	1.0000
SYM	40	-955.9806	2003.1941	0.0000	1.0000
F81	38	-963.2294	2012.5404	0.0000	1.0000
JC69	35	-970.7107	2019.9063	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-925.7738	1931.5476	0.3056	0.3056
HKYI	40	-925.8170	1931.6340	0.2927	0.5983
HKYIG	41	-925.4785	1932.9570	0.1510	0.7493
GTRI	44	-922.9455	1933.8909	0.0947	0.8440
GTRG	44	-922.9476	1933.8953	0.0945	0.9385
GTRIG	45	-922.9474	1935.8948	0.0348	0.9732
K2PG	37	-932.1320	1938.2639	0.0106	0.9839
K2PI	37	-932.1487	1938.2975	0.0105	0.9943
K2PIG	38	-931.9180	1939.8359	0.0048	0.9992
SYMG	41	-931.5677	1945.1354	0.0003	0.9995
SYMI	41	-931.5783	1945.1566	0.0003	0.9999
SYMIG	42	-931.4632	1946.9263	0.0001	1.0000
F81G	39	-938.9583	1955.9167	0.0000	1.0000
F81I	39	-938.9953	1955.9905	0.0000	1.0000
F81IG	40	-938.6848	1957.3697	0.0000	1.0000
JC69G	36	-945.9702	1963.9404	0.0000	1.0000
JC69I	36	-945.9993	1963.9987	0.0000	1.0000
JC69IG	37	-945.6278	1965.2556	0.0000	1.0000
HKY	39	-949.5791	1977.1583	0.0000	1.0000
GTR	43	-946.9952	1979.9905	0.0000	1.0000
K2P	36	-956.8367	1985.6734	0.0000	1.0000
SYM	40	-955.9806	1991.9613	0.0000	1.0000
F81	38	-963.2294	2002.4588	0.0000	1.0000
JC69	35	-970.7107	2011.4214	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-932.1320	2079.1652	0.4456	0.4456
K2PI	37	-932.1487	2079.1988	0.4382	0.8837
HKYG	40	-925.7738	2083.8733	0.0423	0.9261
HKYI	40	-925.8170	2083.9597	0.0405	0.9666
K2PIG	38	-931.9180	2084.5454	0.0302	0.9968
HKYIG	41	-925.4785	2089.0908	0.0031	1.0000
JC69G	36	-945.9702	2101.0335	0.0000	1.0000
JC69I	36	-945.9993	2101.0918	0.0000	1.0000
SYMG	41	-931.5677	2101.2693	0.0000	1.0000
SYMI	41	-931.5783	2101.2904	0.0000	1.0000
GTRI	44	-922.9455	2101.4492	0.0000	1.0000
GTRG	44	-922.9476	2101.4535	0.0000	1.0000
F81G	39	-938.9583	2104.4342	0.0000	1.0000
F81I	39	-938.9953	2104.5081	0.0000	1.0000
JC69IG	37	-945.6278	2106.1569	0.0000	1.0000
SYMIG	42	-931.4632	2106.8683	0.0000	1.0000
GTRIG	45	-922.9474	2107.2612	0.0000	1.0000
F81IG	40	-938.6848	2109.6954	0.0000	1.0000
K2P	36	-956.8367	2122.7665	0.0000	1.0000
HKY	39	-949.5791	2125.6758	0.0000	1.0000
GTR	43	-946.9952	2143.7406	0.0000	1.0000
SYM	40	-955.9806	2144.2870	0.0000	1.0000
JC69	35	-970.7107	2144.7064	0.0000	1.0000
F81	38	-963.2294	2147.1682	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/chr3_14127.phylip = 1 - 333;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_14127.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/chr3_14127.phylip = 1 - 333;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_14127.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/chr3_14127.phylip = 1 - 333;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_14127.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

