
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:28 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/chr1_5479.phylip" (19 taxa, 469 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
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
HKYI	40	-932.9007	1953.4650	0.4137	0.4137
HKYG	40	-932.9071	1953.4777	0.4111	0.8247
HKYIG	41	-932.9066	1955.8788	0.1237	0.9485
GTRI	44	-931.1821	1959.7038	0.0183	0.9668
GTRG	44	-931.2010	1959.7416	0.0179	0.9847
HKY	39	-937.8698	1961.0123	0.0095	0.9942
GTRIG	45	-931.2006	1962.1884	0.0053	0.9995
GTR	43	-936.0853	1967.0742	0.0005	0.9999
F81I	39	-943.8321	1972.9368	0.0000	0.9999
F81G	39	-943.8496	1972.9720	0.0000	1.0000
K2PI	37	-947.2072	1974.9388	0.0000	1.0000
K2PG	37	-947.2256	1974.9755	0.0000	1.0000
F81IG	40	-943.8493	1975.3622	0.0000	1.0000
K2PIG	38	-947.2252	1977.3435	0.0000	1.0000
F81	38	-948.5868	1980.0665	0.0000	1.0000
K2P	36	-951.9292	1982.0251	0.0000	1.0000
SYMI	41	-946.2482	1982.5620	0.0000	1.0000
SYMG	41	-946.2845	1982.6346	0.0000	1.0000
SYMIG	42	-946.2841	1985.0472	0.0000	1.0000
SYM	40	-950.7979	1989.2593	0.0000	1.0000
JC69I	36	-957.0020	1992.1707	0.0000	1.0000
JC69G	36	-957.0216	1992.2098	0.0000	1.0000
JC69IG	37	-957.0211	1994.5666	0.0000	1.0000
JC69	35	-961.6921	1999.2042	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-932.9007	1945.8014	0.3817	0.3817
HKYG	40	-932.9071	1945.8142	0.3793	0.7610
HKYIG	41	-932.9066	1947.8132	0.1396	0.9006
GTRI	44	-931.1821	1950.3642	0.0390	0.9396
GTRG	44	-931.2010	1950.4020	0.0383	0.9779
GTRIG	45	-931.2006	1952.4011	0.0141	0.9919
HKY	39	-937.8698	1953.7396	0.0072	0.9992
GTR	43	-936.0853	1958.1707	0.0008	0.9999
F81I	39	-943.8321	1965.6641	0.0000	1.0000
F81G	39	-943.8496	1965.6993	0.0000	1.0000
F81IG	40	-943.8493	1967.6986	0.0000	1.0000
K2PI	37	-947.2072	1968.4145	0.0000	1.0000
K2PG	37	-947.2256	1968.4512	0.0000	1.0000
K2PIG	38	-947.2252	1970.4505	0.0000	1.0000
F81	38	-948.5868	1973.1735	0.0000	1.0000
SYMI	41	-946.2482	1974.4965	0.0000	1.0000
SYMG	41	-946.2845	1974.5690	0.0000	1.0000
K2P	36	-951.9292	1975.8584	0.0000	1.0000
SYMIG	42	-946.2841	1976.5683	0.0000	1.0000
SYM	40	-950.7979	1981.5958	0.0000	1.0000
JC69I	36	-957.0020	1986.0040	0.0000	1.0000
JC69G	36	-957.0216	1986.0432	0.0000	1.0000
JC69IG	37	-957.0211	1988.0423	0.0000	1.0000
JC69	35	-961.6921	1993.3843	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-932.9007	2111.8255	0.4536	0.4536
HKYG	40	-932.9071	2111.8383	0.4507	0.9042
HKY	39	-937.8698	2115.6131	0.0683	0.9725
HKYIG	41	-932.9066	2117.9879	0.0208	0.9933
K2PI	37	-947.2072	2121.9868	0.0028	0.9961
K2PG	37	-947.2256	2122.0235	0.0028	0.9989
K2P	36	-951.9292	2125.2801	0.0005	0.9995
F81I	39	-943.8321	2127.5376	0.0002	0.9996
F81G	39	-943.8496	2127.5728	0.0002	0.9998
K2PIG	38	-947.2252	2128.1734	0.0001	0.9999
F81	38	-948.5868	2130.8964	0.0000	1.0000
GTRI	44	-931.1821	2132.9907	0.0000	1.0000
GTRG	44	-931.2010	2133.0285	0.0000	1.0000
F81IG	40	-943.8493	2133.7227	0.0000	1.0000
JC69I	36	-957.0020	2135.4257	0.0000	1.0000
JC69G	36	-957.0216	2135.4649	0.0000	1.0000
GTR	43	-936.0853	2136.6466	0.0000	1.0000
JC69	35	-961.6921	2138.6554	0.0000	1.0000
GTRIG	45	-931.2006	2139.1783	0.0000	1.0000
JC69IG	37	-957.0211	2141.6146	0.0000	1.0000
SYMI	41	-946.2482	2144.6712	0.0000	1.0000
SYMG	41	-946.2845	2144.7438	0.0000	1.0000
SYM	40	-950.7979	2147.6199	0.0000	1.0000
SYMIG	42	-946.2841	2150.8936	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5479.phylip = 1 - 469;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5479.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;


[Mrbayes block for the best AICc model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5479.phylip = 1 - 469;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5479.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;


[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/chr1_5479.phylip = 1 - 469;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5479.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;


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End of Output

