
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:21 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_11540.phylip" (19 taxa, 624 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: GTRG


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
GTRG	44	-1929.8496	3954.5386	0.5704	0.5704
GTRI	44	-1930.6766	3956.1925	0.2495	0.8198
GTRIG	45	-1929.8494	3956.8614	0.1786	0.9984
GTR	43	-1936.9575	3966.4391	0.0015	0.9999
HKYG	40	-1943.3421	3972.3102	0.0001	0.9999
HKYI	40	-1944.0796	3973.7853	0.0000	1.0000
HKYIG	41	-1943.3464	3974.6102	0.0000	1.0000
HKY	39	-1950.6301	3984.6026	0.0000	1.0000
SYMG	41	-1958.6321	4005.1817	0.0000	1.0000
SYMI	41	-1959.2825	4006.4826	0.0000	1.0000
SYMIG	42	-1958.6469	4007.5107	0.0000	1.0000
K2PG	37	-1964.7913	4008.3813	0.0000	1.0000
K2PI	37	-1965.5292	4009.8571	0.0000	1.0000
K2PIG	38	-1964.7964	4010.6595	0.0000	1.0000
SYM	40	-1966.0341	4017.6944	0.0000	1.0000
K2P	36	-1973.0412	4022.6207	0.0000	1.0000
F81G	39	-1973.8024	4030.9473	0.0000	1.0000
F81I	39	-1974.4731	4032.2887	0.0000	1.0000
F81IG	40	-1973.8145	4033.2550	0.0000	1.0000
F81	38	-1981.0665	4043.1997	0.0000	1.0000
JC69G	36	-1992.5958	4061.7299	0.0000	1.0000
JC69I	36	-1993.2500	4063.0383	0.0000	1.0000
JC69IG	37	-1992.6149	4064.0284	0.0000	1.0000
JC69	35	-2000.5432	4075.3722	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1929.8496	3947.6993	0.5532	0.5532
GTRI	44	-1930.6766	3949.3532	0.2420	0.7951
GTRIG	45	-1929.8494	3949.6988	0.2036	0.9987
GTR	43	-1936.9575	3959.9150	0.0012	0.9999
HKYG	40	-1943.3421	3966.6842	0.0000	1.0000
HKYI	40	-1944.0796	3968.1592	0.0000	1.0000
HKYIG	41	-1943.3464	3968.6927	0.0000	1.0000
HKY	39	-1950.6301	3979.2602	0.0000	1.0000
SYMG	41	-1958.6321	3999.2642	0.0000	1.0000
SYMI	41	-1959.2825	4000.5651	0.0000	1.0000
SYMIG	42	-1958.6469	4001.2939	0.0000	1.0000
K2PG	37	-1964.7913	4003.5826	0.0000	1.0000
K2PI	37	-1965.5292	4005.0585	0.0000	1.0000
K2PIG	38	-1964.7964	4005.5929	0.0000	1.0000
SYM	40	-1966.0341	4012.0683	0.0000	1.0000
K2P	36	-1973.0412	4018.0824	0.0000	1.0000
F81G	39	-1973.8024	4025.6049	0.0000	1.0000
F81I	39	-1974.4731	4026.9463	0.0000	1.0000
F81IG	40	-1973.8145	4027.6290	0.0000	1.0000
F81	38	-1981.0665	4038.1331	0.0000	1.0000
JC69G	36	-1992.5958	4057.1915	0.0000	1.0000
JC69I	36	-1993.2500	4058.5000	0.0000	1.0000
JC69IG	37	-1992.6149	4059.2297	0.0000	1.0000
JC69	35	-2000.5432	4071.0865	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-1929.8496	4142.8899	0.4304	0.4304
HKYG	40	-1943.3421	4144.1302	0.2315	0.6618
GTRI	44	-1930.6766	4144.5438	0.1882	0.8501
HKYI	40	-1944.0796	4145.6052	0.1107	0.9608
GTRIG	45	-1929.8494	4149.3256	0.0172	0.9780
HKYIG	41	-1943.3464	4150.5749	0.0092	0.9872
GTR	43	-1936.9575	4150.6694	0.0088	0.9960
HKY	39	-1950.6301	4152.2700	0.0040	1.0000
K2PG	37	-1964.7913	4167.7202	0.0000	1.0000
K2PI	37	-1965.5292	4169.1960	0.0000	1.0000
K2PIG	38	-1964.7964	4174.1666	0.0000	1.0000
K2P	36	-1973.0412	4177.7838	0.0000	1.0000
SYMG	41	-1958.6321	4181.1464	0.0000	1.0000
SYMI	41	-1959.2825	4182.4473	0.0000	1.0000
SYMIG	42	-1958.6469	4187.6122	0.0000	1.0000
SYM	40	-1966.0341	4189.5143	0.0000	1.0000
F81G	39	-1973.8024	4198.6147	0.0000	1.0000
F81I	39	-1974.4731	4199.9561	0.0000	1.0000
F81IG	40	-1973.8145	4205.0750	0.0000	1.0000
F81	38	-1981.0665	4206.7068	0.0000	1.0000
JC69G	36	-1992.5958	4216.8929	0.0000	1.0000
JC69I	36	-1993.2500	4218.2014	0.0000	1.0000
JC69IG	37	-1992.6149	4223.3673	0.0000	1.0000
JC69	35	-2000.5432	4226.3518	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11540.phylip = 1 - 624;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11540.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11540.phylip = 1 - 624;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11540.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best BIC model (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11540.phylip = 1 - 624;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11540.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

