
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:37 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_10184.phylip" (19 taxa, 332 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-935.0056	1971.8091	0.4004	0.4004
GTRI	44	-935.3778	1972.5535	0.2759	0.6763
HKYG	40	-941.4920	1974.2555	0.1178	0.7941
GTRIG	45	-935.1010	1974.6776	0.0954	0.8895
HKYI	40	-941.8373	1974.9460	0.0834	0.9729
HKYIG	41	-941.6622	1977.2004	0.0270	1.0000
SYMG	41	-949.0334	1991.9426	0.0000	1.0000
SYMI	41	-949.4572	1992.7903	0.0000	1.0000
SYMIG	42	-949.0246	1994.5475	0.0000	1.0000
K2PG	37	-956.6839	1996.9323	0.0000	1.0000
K2PI	37	-956.6960	1996.9566	0.0000	1.0000
K2PIG	38	-956.4861	1999.0882	0.0000	1.0000
F81G	39	-965.8849	2020.4547	0.0000	1.0000
F81I	39	-965.8954	2020.4758	0.0000	1.0000
F81IG	40	-965.7747	2022.8210	0.0000	1.0000
GTR	43	-962.1426	2023.4240	0.0000	1.0000
HKY	39	-968.7202	2026.1254	0.0000	1.0000
JC69G	36	-979.8027	2040.6360	0.0000	1.0000
JC69I	36	-979.8296	2040.6897	0.0000	1.0000
JC69IG	37	-979.6624	2042.8894	0.0000	1.0000
SYM	40	-977.7745	2046.8205	0.0000	1.0000
K2P	36	-982.9378	2046.9061	0.0000	1.0000
F81	38	-991.0290	2068.1741	0.0000	1.0000
JC69	35	-1004.5843	2087.6821	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-935.0056	1958.0112	0.4563	0.4563
GTRI	44	-935.3778	1958.7556	0.3145	0.7708
GTRIG	45	-935.1010	1960.2021	0.1526	0.9234
HKYG	40	-941.4920	1962.9841	0.0380	0.9613
HKYI	40	-941.8373	1963.6745	0.0269	0.9882
HKYIG	41	-941.6622	1965.3245	0.0118	1.0000
SYMG	41	-949.0334	1980.0667	0.0000	1.0000
SYMI	41	-949.4572	1980.9144	0.0000	1.0000
SYMIG	42	-949.0246	1982.0492	0.0000	1.0000
K2PG	37	-956.6839	1987.3677	0.0000	1.0000
K2PI	37	-956.6960	1987.3920	0.0000	1.0000
K2PIG	38	-956.4861	1988.9722	0.0000	1.0000
F81G	39	-965.8849	2009.7698	0.0000	1.0000
F81I	39	-965.8954	2009.7908	0.0000	1.0000
GTR	43	-962.1426	2010.2852	0.0000	1.0000
F81IG	40	-965.7747	2011.5495	0.0000	1.0000
HKY	39	-968.7202	2015.4405	0.0000	1.0000
JC69G	36	-979.8027	2031.6055	0.0000	1.0000
JC69I	36	-979.8296	2031.6592	0.0000	1.0000
JC69IG	37	-979.6624	2033.3248	0.0000	1.0000
SYM	40	-977.7745	2035.5490	0.0000	1.0000
K2P	36	-982.9378	2037.8756	0.0000	1.0000
F81	38	-991.0290	2058.0580	0.0000	1.0000
JC69	35	-1004.5843	2079.1686	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-941.4920	2115.1895	0.5656	0.5656
HKYI	40	-941.8373	2115.8799	0.4005	0.9662
HKYIG	41	-941.6622	2121.3350	0.0262	0.9923
GTRG	44	-935.0056	2125.4372	0.0034	0.9957
GTRI	44	-935.3778	2126.1816	0.0023	0.9980
K2PG	37	-956.6839	2128.1577	0.0009	0.9989
K2PI	37	-956.6960	2128.1820	0.0009	0.9997
GTRIG	45	-935.1010	2131.4332	0.0002	0.9999
K2PIG	38	-956.4861	2133.5673	0.0001	1.0000
SYMG	41	-949.0334	2136.0772	0.0000	1.0000
SYMI	41	-949.4572	2136.9250	0.0000	1.0000
SYMIG	42	-949.0246	2141.8649	0.0000	1.0000
F81G	39	-965.8849	2158.1700	0.0000	1.0000
F81I	39	-965.8954	2158.1911	0.0000	1.0000
F81IG	40	-965.7747	2163.7549	0.0000	1.0000
HKY	39	-968.7202	2163.8408	0.0000	1.0000
JC69G	36	-979.8027	2168.5903	0.0000	1.0000
JC69I	36	-979.8296	2168.6441	0.0000	1.0000
GTR	43	-962.1426	2173.9060	0.0000	1.0000
JC69IG	37	-979.6624	2174.1148	0.0000	1.0000
K2P	36	-982.9378	2174.8604	0.0000	1.0000
SYM	40	-977.7745	2187.7544	0.0000	1.0000
F81	38	-991.0290	2202.6532	0.0000	1.0000
JC69	35	-1004.5843	2212.3483	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/chr5_10184.phylip = 1 - 332;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10184.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/chr5_10184.phylip = 1 - 332;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10184.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10184.phylip = 1 - 332;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10184.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

