
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:26 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/chr5_11269.phylip" (19 taxa, 403 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	-921.1397	1931.3402	0.4599	0.4599
HKYG	40	-921.6116	1932.2840	0.2869	0.7468
HKYIG	41	-921.1346	1933.8093	0.1338	0.8806
GTRI	44	-918.2008	1935.4631	0.0585	0.9391
GTRG	44	-918.5322	1936.1260	0.0420	0.9811
GTRIG	45	-918.0650	1937.7266	0.0189	1.0000
K2PI	37	-938.0913	1957.8866	0.0000	1.0000
K2PG	37	-938.7122	1959.1284	0.0000	1.0000
K2PIG	38	-937.9457	1960.0343	0.0000	1.0000
F81I	39	-936.8010	1960.1970	0.0000	1.0000
F81G	39	-937.1308	1960.8567	0.0000	1.0000
SYMG	41	-935.1883	1961.9167	0.0000	1.0000
F81IG	40	-936.6633	1962.3875	0.0000	1.0000
HKY	39	-938.0083	1962.6116	0.0000	1.0000
SYMI	41	-936.6502	1964.8405	0.0000	1.0000
GTR	43	-934.9341	1966.4085	0.0000	1.0000
SYMIG	42	-936.2220	1966.4773	0.0000	1.0000
JC69I	36	-952.2827	1983.8441	0.0000	1.0000
JC69G	36	-952.6921	1984.6628	0.0000	1.0000
JC69IG	37	-952.0528	1985.8097	0.0000	1.0000
F81	38	-952.8560	1989.8548	0.0000	1.0000
K2P	36	-955.3978	1990.0743	0.0000	1.0000
SYM	40	-951.3861	1991.8330	0.0000	1.0000
JC69	35	-968.7110	2014.2884	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-921.1397	1922.2794	0.3658	0.3658
HKYG	40	-921.6116	1923.2232	0.2282	0.5940
HKYIG	41	-921.1346	1924.2692	0.1353	0.7292
GTRI	44	-918.2008	1924.4016	0.1266	0.8558
GTRG	44	-918.5322	1925.0645	0.0909	0.9467
GTRIG	45	-918.0650	1926.1300	0.0533	1.0000
K2PI	37	-938.0913	1950.1825	0.0000	1.0000
K2PG	37	-938.7122	1951.4243	0.0000	1.0000
F81I	39	-936.8010	1951.6019	0.0000	1.0000
K2PIG	38	-937.9457	1951.8915	0.0000	1.0000
F81G	39	-937.1308	1952.2616	0.0000	1.0000
SYMG	41	-935.1883	1952.3766	0.0000	1.0000
F81IG	40	-936.6633	1953.3267	0.0000	1.0000
HKY	39	-938.0083	1954.0165	0.0000	1.0000
SYMI	41	-936.6502	1955.3003	0.0000	1.0000
GTR	43	-934.9341	1955.8681	0.0000	1.0000
SYMIG	42	-936.2220	1956.4440	0.0000	1.0000
JC69I	36	-952.2827	1976.5654	0.0000	1.0000
JC69G	36	-952.6921	1977.3842	0.0000	1.0000
JC69IG	37	-952.0528	1978.1056	0.0000	1.0000
F81	38	-952.8560	1981.7120	0.0000	1.0000
SYM	40	-951.3861	1982.7722	0.0000	1.0000
K2P	36	-955.3978	1982.7956	0.0000	1.0000
JC69	35	-968.7110	2007.4219	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-921.1397	2082.2369	0.5971	0.5971
HKYG	40	-921.6116	2083.1806	0.3725	0.9696
HKYIG	41	-921.1346	2088.2256	0.0299	0.9995
K2PI	37	-938.0913	2098.1432	0.0002	0.9997
K2PG	37	-938.7122	2099.3850	0.0001	0.9999
GTRI	44	-918.2008	2100.3548	0.0001	0.9999
GTRG	44	-918.5322	2101.0177	0.0000	1.0000
K2PIG	38	-937.9457	2103.8511	0.0000	1.0000
GTRIG	45	-918.0650	2106.0821	0.0000	1.0000
F81I	39	-936.8010	2107.5605	0.0000	1.0000
F81G	39	-937.1308	2108.2202	0.0000	1.0000
HKY	39	-938.0083	2109.9750	0.0000	1.0000
F81IG	40	-936.6633	2113.2841	0.0000	1.0000
SYMG	41	-935.1883	2116.3330	0.0000	1.0000
SYMI	41	-936.6502	2119.2567	0.0000	1.0000
JC69I	36	-952.2827	2120.5271	0.0000	1.0000
JC69G	36	-952.6921	2121.3459	0.0000	1.0000
SYMIG	42	-936.2220	2124.3993	0.0000	1.0000
JC69IG	37	-952.0528	2126.0663	0.0000	1.0000
K2P	36	-955.3978	2126.7573	0.0000	1.0000
GTR	43	-934.9341	2127.8224	0.0000	1.0000
F81	38	-952.8560	2133.6715	0.0000	1.0000
SYM	40	-951.3861	2142.7297	0.0000	1.0000
JC69	35	-968.7110	2147.3847	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/chr5_11269.phylip = 1 - 403;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11269.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/chr5_11269.phylip = 1 - 403;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11269.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/chr5_11269.phylip = 1 - 403;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11269.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

