
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:14 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_4736.phylip" (19 taxa, 342 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYG
Minimum BIC  model: HKYG


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	-919.3923	1929.6816	0.4261	0.4261
HKYIG	41	-918.3453	1930.1707	0.3337	0.7598
HKYI	40	-920.1889	1931.2747	0.1921	0.9520
GTRG	44	-917.1378	1935.6090	0.0220	0.9740
GTRIG	45	-916.0643	1936.1150	0.0171	0.9911
GTRI	44	-918.0386	1937.4105	0.0089	1.0000
HKY	39	-938.0522	1964.4355	0.0000	1.0000
GTR	43	-935.6194	1969.9369	0.0000	1.0000
F81IG	40	-940.7377	1972.3724	0.0000	1.0000
F81G	39	-942.8837	1974.0985	0.0000	1.0000
K2PG	37	-945.9634	1975.1768	0.0000	1.0000
K2PIG	38	-944.8546	1975.4913	0.0000	1.0000
F81I	39	-943.7201	1975.7713	0.0000	1.0000
K2PI	37	-946.7877	1976.8254	0.0000	1.0000
SYMG	41	-944.5350	1982.5500	0.0000	1.0000
SYMIG	42	-943.2514	1982.5830	0.0000	1.0000
SYMI	41	-945.4164	1984.3128	0.0000	1.0000
F81	38	-961.1540	2008.0901	0.0000	1.0000
K2P	36	-964.0725	2008.8795	0.0000	1.0000
SYM	40	-962.8908	2016.6785	0.0000	1.0000
JC69IG	37	-966.8211	2016.8921	0.0000	1.0000
JC69G	36	-968.8149	2018.3642	0.0000	1.0000
JC69I	36	-969.6072	2019.9487	0.0000	1.0000
JC69	35	-986.9296	2052.0946	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-918.3453	1918.6907	0.3574	0.3574
HKYG	40	-919.3923	1918.7846	0.3410	0.6985
HKYI	40	-920.1889	1920.3777	0.1538	0.8522
GTRIG	45	-916.0643	1922.1285	0.0641	0.9163
GTRG	44	-917.1378	1922.2756	0.0595	0.9758
GTRI	44	-918.0386	1924.0772	0.0242	1.0000
HKY	39	-938.0522	1954.1044	0.0000	1.0000
GTR	43	-935.6194	1957.2389	0.0000	1.0000
F81IG	40	-940.7377	1961.4754	0.0000	1.0000
F81G	39	-942.8837	1963.7674	0.0000	1.0000
F81I	39	-943.7201	1965.4402	0.0000	1.0000
K2PIG	38	-944.8546	1965.7091	0.0000	1.0000
K2PG	37	-945.9634	1965.9268	0.0000	1.0000
K2PI	37	-946.7877	1967.5754	0.0000	1.0000
SYMIG	42	-943.2514	1970.5027	0.0000	1.0000
SYMG	41	-944.5350	1971.0700	0.0000	1.0000
SYMI	41	-945.4164	1972.8328	0.0000	1.0000
F81	38	-961.1540	1998.3080	0.0000	1.0000
K2P	36	-964.0725	2000.1451	0.0000	1.0000
SYM	40	-962.8908	2005.7815	0.0000	1.0000
JC69IG	37	-966.8211	2007.6421	0.0000	1.0000
JC69G	36	-968.8149	2009.6298	0.0000	1.0000
JC69I	36	-969.6072	2011.2143	0.0000	1.0000
JC69	35	-986.9296	2043.8593	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-919.3923	2072.1770	0.6230	0.6230
HKYI	40	-920.1889	2073.7701	0.2809	0.9039
HKYIG	41	-918.3453	2075.9179	0.0960	0.9999
GTRG	44	-917.1378	2091.0073	0.0001	1.0000
GTRI	44	-918.0386	2092.8089	0.0000	1.0000
GTRIG	45	-916.0643	2094.6950	0.0000	1.0000
HKY	39	-938.0522	2103.6620	0.0000	1.0000
K2PG	37	-945.9634	2107.8148	0.0000	1.0000
K2PI	37	-946.7877	2109.4634	0.0000	1.0000
K2PIG	38	-944.8546	2111.4319	0.0000	1.0000
F81G	39	-942.8837	2113.3250	0.0000	1.0000
F81IG	40	-940.7377	2114.8678	0.0000	1.0000
F81I	39	-943.7201	2114.9978	0.0000	1.0000
GTR	43	-935.6194	2122.1357	0.0000	1.0000
SYMG	41	-944.5350	2128.2972	0.0000	1.0000
SYMI	41	-945.4164	2130.0600	0.0000	1.0000
SYMIG	42	-943.2514	2131.5648	0.0000	1.0000
K2P	36	-964.0725	2138.1983	0.0000	1.0000
F81	38	-961.1540	2144.0308	0.0000	1.0000
JC69G	36	-968.8149	2147.6830	0.0000	1.0000
JC69I	36	-969.6072	2149.2675	0.0000	1.0000
JC69IG	37	-966.8211	2149.5301	0.0000	1.0000
SYM	40	-962.8908	2159.1740	0.0000	1.0000
JC69	35	-986.9296	2178.0777	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4736.phylip = 1 - 342;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4736.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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_4736.phylip = 1 - 342;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4736.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4736.phylip = 1 - 342;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4736.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;


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End of Output

