
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:29 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/chr22_491.phylip" (19 taxa, 299 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	-971.5778	2046.7462	0.8666	0.8666
HKYG	40	-979.5438	2051.8008	0.0692	0.9358
GTRIG	45	-973.1881	2052.7398	0.0433	0.9791
GTRI	44	-975.5760	2054.7425	0.0159	0.9950
HKYIG	41	-981.2634	2057.9275	0.0032	0.9982
HKYI	40	-983.2176	2059.1484	0.0018	1.0000
SYMG	41	-988.1094	2071.6196	0.0000	1.0000
K2PG	37	-993.5027	2071.7794	0.0000	1.0000
K2PIG	38	-992.5756	2072.5511	0.0000	1.0000
SYMIG	42	-987.4597	2073.0288	0.0000	1.0000
K2PI	37	-994.6045	2073.9829	0.0000	1.0000
SYMI	41	-989.6391	2074.6790	0.0000	1.0000
HKY	39	-996.1801	2082.4065	0.0000	1.0000
GTR	43	-991.2141	2083.2673	0.0000	1.0000
F81G	39	-1000.4312	2090.9088	0.0000	1.0000
F81I	39	-1000.8323	2091.7110	0.0000	1.0000
F81IG	40	-1003.5512	2099.8155	0.0000	1.0000
SYM	40	-1003.9734	2100.6600	0.0000	1.0000
K2P	36	-1012.2558	2106.6795	0.0000	1.0000
JC69G	36	-1013.1138	2108.3955	0.0000	1.0000
JC69IG	37	-1012.9002	2110.5744	0.0000	1.0000
JC69I	36	-1017.1991	2116.5660	0.0000	1.0000
F81	38	-1019.7088	2126.8175	0.0000	1.0000
JC69	35	-1034.1632	2147.9081	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-971.5778	2031.1557	0.8988	0.8988
GTRIG	45	-973.1881	2036.3762	0.0661	0.9649
HKYG	40	-979.5438	2039.0876	0.0170	0.9819
GTRI	44	-975.5760	2039.1520	0.0165	0.9984
HKYIG	41	-981.2634	2044.5267	0.0011	0.9996
HKYI	40	-983.2176	2046.4352	0.0004	1.0000
SYMG	41	-988.1094	2058.2188	0.0000	1.0000
SYMIG	42	-987.4597	2058.9194	0.0000	1.0000
K2PG	37	-993.5027	2061.0055	0.0000	1.0000
K2PIG	38	-992.5756	2061.1511	0.0000	1.0000
SYMI	41	-989.6391	2061.2782	0.0000	1.0000
K2PI	37	-994.6045	2063.2089	0.0000	1.0000
GTR	43	-991.2141	2068.4281	0.0000	1.0000
HKY	39	-996.1801	2070.3602	0.0000	1.0000
F81G	39	-1000.4312	2078.8624	0.0000	1.0000
F81I	39	-1000.8323	2079.6646	0.0000	1.0000
F81IG	40	-1003.5512	2087.1023	0.0000	1.0000
SYM	40	-1003.9734	2087.9468	0.0000	1.0000
K2P	36	-1012.2558	2096.5116	0.0000	1.0000
JC69G	36	-1013.1138	2098.2275	0.0000	1.0000
JC69IG	37	-1012.9002	2099.8004	0.0000	1.0000
JC69I	36	-1017.1991	2106.3981	0.0000	1.0000
F81	38	-1019.7088	2115.4175	0.0000	1.0000
JC69	35	-1034.1632	2138.3264	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-979.5438	2187.1054	0.9297	0.9297
GTRG	44	-971.5778	2193.9752	0.0300	0.9597
HKYI	40	-983.2176	2194.4530	0.0236	0.9833
HKYIG	41	-981.2634	2196.2449	0.0096	0.9929
K2PG	37	-993.5027	2197.9219	0.0042	0.9971
K2PI	37	-994.6045	2200.1254	0.0014	0.9985
K2PIG	38	-992.5756	2201.7680	0.0006	0.9991
GTRI	44	-975.5760	2201.9715	0.0005	0.9996
GTRIG	45	-973.1881	2202.8961	0.0003	1.0000
SYMG	41	-988.1094	2209.9370	0.0000	1.0000
SYMI	41	-989.6391	2212.9964	0.0000	1.0000
SYMIG	42	-987.4597	2214.3380	0.0000	1.0000
HKY	39	-996.1801	2214.6775	0.0000	1.0000
F81G	39	-1000.4312	2223.1797	0.0000	1.0000
F81I	39	-1000.8323	2223.9819	0.0000	1.0000
GTR	43	-991.2141	2227.5472	0.0000	1.0000
K2P	36	-1012.2558	2229.7275	0.0000	1.0000
JC69G	36	-1013.1138	2231.4435	0.0000	1.0000
F81IG	40	-1003.5512	2235.1201	0.0000	1.0000
SYM	40	-1003.9734	2235.9645	0.0000	1.0000
JC69IG	37	-1012.9002	2236.7169	0.0000	1.0000
JC69I	36	-1017.1991	2239.6141	0.0000	1.0000
F81	38	-1019.7088	2256.0344	0.0000	1.0000
JC69	35	-1034.1632	2267.8419	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/chr22_491.phylip = 1 - 299;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr22_491.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/chr22_491.phylip = 1 - 299;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr22_491.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/chr22_491.phylip = 1 - 299;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr22_491.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

