
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:37 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/chr1_20864.phylip" (19 taxa, 272 characters)

Minimum AIC  model: GTRG
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	-942.6523	1979.5038	0.5019	0.5019
GTRG	44	-937.8923	1981.2296	0.2118	0.7136
HKYIG	41	-942.6521	1982.2782	0.1254	0.8390
HKYI	40	-944.6204	1983.4399	0.0701	0.9091
GTRIG	45	-937.8923	1984.1031	0.0503	0.9595
GTRI	44	-939.8542	1985.1534	0.0298	0.9892
HKY	39	-948.4739	1988.3961	0.0059	0.9951
GTR	43	-943.0848	1988.7661	0.0049	1.0000
K2PG	37	-962.5574	2011.1319	0.0000	1.0000
K2PIG	38	-962.5439	2013.8089	0.0000	1.0000
K2PI	37	-964.4468	2014.9107	0.0000	1.0000
SYMG	41	-961.0058	2018.9855	0.0000	1.0000
SYMIG	42	-961.0026	2021.7782	0.0000	1.0000
SYMI	41	-962.9384	2022.8508	0.0000	1.0000
K2P	36	-970.4104	2024.1570	0.0000	1.0000
F81G	39	-966.9214	2025.2911	0.0000	1.0000
F81IG	40	-966.9212	2028.0416	0.0000	1.0000
F81I	39	-968.5274	2028.5032	0.0000	1.0000
SYM	40	-968.0989	2030.3969	0.0000	1.0000
F81	38	-973.0275	2034.7760	0.0000	1.0000
JC69G	36	-982.9709	2049.2779	0.0000	1.0000
JC69IG	37	-982.9634	2051.9439	0.0000	1.0000
JC69I	36	-984.7335	2052.8032	0.0000	1.0000
JC69	35	-990.3337	2061.3453	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-937.8923	1963.7846	0.4479	0.4479
HKYG	40	-942.6523	1965.3047	0.2095	0.6574
GTRIG	45	-937.8923	1965.7845	0.1648	0.8222
HKYIG	41	-942.6521	1967.3043	0.0771	0.8993
GTRI	44	-939.8542	1967.7085	0.0630	0.9623
HKYI	40	-944.6204	1969.2408	0.0293	0.9915
GTR	43	-943.0848	1972.1696	0.0068	0.9983
HKY	39	-948.4739	1974.9478	0.0017	1.0000
K2PG	37	-962.5574	1999.1148	0.0000	1.0000
K2PIG	38	-962.5439	2001.0878	0.0000	1.0000
K2PI	37	-964.4468	2002.8936	0.0000	1.0000
SYMG	41	-961.0058	2004.0116	0.0000	1.0000
SYMIG	42	-961.0026	2006.0053	0.0000	1.0000
SYMI	41	-962.9384	2007.8769	0.0000	1.0000
F81G	39	-966.9214	2011.8428	0.0000	1.0000
K2P	36	-970.4104	2012.8208	0.0000	1.0000
F81IG	40	-966.9212	2013.8425	0.0000	1.0000
F81I	39	-968.5274	2015.0549	0.0000	1.0000
SYM	40	-968.0989	2016.1978	0.0000	1.0000
F81	38	-973.0275	2022.0549	0.0000	1.0000
JC69G	36	-982.9709	2037.9418	0.0000	1.0000
JC69IG	37	-982.9634	2039.9268	0.0000	1.0000
JC69I	36	-984.7335	2041.4670	0.0000	1.0000
JC69	35	-990.3337	2050.6673	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-942.6523	2109.5367	0.7992	0.7992
HKYI	40	-944.6204	2113.4728	0.1117	0.9108
HKYIG	41	-942.6521	2115.1422	0.0485	0.9593
HKY	39	-948.4739	2115.5741	0.0391	0.9984
GTRG	44	-937.8923	2122.4399	0.0013	0.9996
GTRI	44	-939.8542	2126.3638	0.0002	0.9998
GTR	43	-943.0848	2127.2191	0.0001	0.9999
GTRIG	45	-937.8923	2128.0456	0.0001	1.0000
K2PG	37	-962.5574	2132.5295	0.0000	1.0000
K2PI	37	-964.4468	2136.3083	0.0000	1.0000
K2PIG	38	-962.5439	2138.1083	0.0000	1.0000
K2P	36	-970.4104	2142.6297	0.0000	1.0000
SYMG	41	-961.0058	2151.8494	0.0000	1.0000
F81G	39	-966.9214	2152.4691	0.0000	1.0000
F81I	39	-968.5274	2155.6812	0.0000	1.0000
SYMI	41	-962.9384	2155.7147	0.0000	1.0000
SYMIG	42	-961.0026	2157.4490	0.0000	1.0000
F81IG	40	-966.9212	2158.0746	0.0000	1.0000
F81	38	-973.0275	2159.0754	0.0000	1.0000
SYM	40	-968.0989	2160.4299	0.0000	1.0000
JC69G	36	-982.9709	2167.7506	0.0000	1.0000
JC69I	36	-984.7335	2171.2759	0.0000	1.0000
JC69IG	37	-982.9634	2173.3415	0.0000	1.0000
JC69	35	-990.3337	2176.8704	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/chr1_20864.phylip = 1 - 272;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_20864.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_20864.phylip = 1 - 272;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_20864.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/chr1_20864.phylip = 1 - 272;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_20864.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

