
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:28 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/chr3_7252.phylip" (19 taxa, 275 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	-933.4976	1961.0124	0.2934	0.2934
GTRG	44	-927.9320	1961.0814	0.2834	0.5768
GTRI	44	-928.5879	1962.3931	0.1471	0.7239
HKYI	40	-934.3262	1962.6694	0.1281	0.8520
HKYIG	41	-933.4149	1963.6109	0.0800	0.9320
GTRIG	45	-927.9308	1963.9401	0.0679	0.9999
K2PG	37	-946.2336	1978.3322	0.0001	1.0000
K2PI	37	-947.1939	1980.2527	0.0000	1.0000
K2PIG	38	-946.0684	1980.6961	0.0000	1.0000
SYMG	41	-943.5119	1983.8050	0.0000	1.0000
SYMI	41	-944.2196	1985.2204	0.0000	1.0000
SYMIG	42	-943.4474	1986.4637	0.0000	1.0000
HKY	39	-955.7827	2002.8420	0.0000	1.0000
GTR	43	-951.8214	2006.0237	0.0000	1.0000
K2P	36	-967.3155	2017.8243	0.0000	1.0000
SYM	40	-965.0661	2024.1493	0.0000	1.0000
F81G	39	-967.3415	2025.9596	0.0000	1.0000
F81I	39	-968.2074	2027.6915	0.0000	1.0000
F81IG	40	-967.2431	2028.5033	0.0000	1.0000
JC69G	36	-975.9162	2035.0256	0.0000	1.0000
JC69I	36	-976.8291	2036.8514	0.0000	1.0000
JC69IG	37	-975.7976	2037.4602	0.0000	1.0000
F81	38	-988.2781	2065.1155	0.0000	1.0000
JC69	35	-996.5148	2073.5735	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-927.9320	1943.8640	0.4403	0.4403
GTRI	44	-928.5879	1945.1757	0.2285	0.6688
GTRIG	45	-927.9308	1945.8615	0.1622	0.8310
HKYG	40	-933.4976	1946.9953	0.0920	0.9230
HKYI	40	-934.3262	1948.6523	0.0402	0.9632
HKYIG	41	-933.4149	1948.8298	0.0368	1.0000
K2PG	37	-946.2336	1966.4672	0.0000	1.0000
K2PIG	38	-946.0684	1968.1368	0.0000	1.0000
K2PI	37	-947.1939	1968.3877	0.0000	1.0000
SYMG	41	-943.5119	1969.0239	0.0000	1.0000
SYMI	41	-944.2196	1970.4393	0.0000	1.0000
SYMIG	42	-943.4474	1970.8947	0.0000	1.0000
HKY	39	-955.7827	1989.5654	0.0000	1.0000
GTR	43	-951.8214	1989.6427	0.0000	1.0000
K2P	36	-967.3155	2006.6310	0.0000	1.0000
SYM	40	-965.0661	2010.1322	0.0000	1.0000
F81G	39	-967.3415	2012.6830	0.0000	1.0000
F81I	39	-968.2074	2014.4149	0.0000	1.0000
F81IG	40	-967.2431	2014.4862	0.0000	1.0000
JC69G	36	-975.9162	2023.8323	0.0000	1.0000
JC69IG	37	-975.7976	2025.5952	0.0000	1.0000
JC69I	36	-976.8291	2025.6582	0.0000	1.0000
F81	38	-988.2781	2052.5562	0.0000	1.0000
JC69	35	-996.5148	2063.0296	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-933.4976	2091.6661	0.6548	0.6548
HKYI	40	-934.3262	2093.3232	0.2859	0.9408
HKYIG	41	-933.4149	2097.1174	0.0429	0.9836
K2PG	37	-946.2336	2100.2878	0.0088	0.9924
K2PI	37	-947.1939	2102.2083	0.0034	0.9958
GTRG	44	-927.9320	2103.0019	0.0023	0.9981
GTRI	44	-928.5879	2104.3136	0.0012	0.9992
K2PIG	38	-946.0684	2105.5741	0.0006	0.9999
GTRIG	45	-927.9308	2108.6162	0.0001	1.0000
SYMG	41	-943.5119	2117.3115	0.0000	1.0000
SYMI	41	-944.2196	2118.7269	0.0000	1.0000
SYMIG	42	-943.4474	2122.7991	0.0000	1.0000
HKY	39	-955.7827	2130.6195	0.0000	1.0000
K2P	36	-967.3155	2136.8348	0.0000	1.0000
GTR	43	-951.8214	2145.1639	0.0000	1.0000
F81G	39	-967.3415	2153.7370	0.0000	1.0000
JC69G	36	-975.9162	2154.0361	0.0000	1.0000
SYM	40	-965.0661	2154.8030	0.0000	1.0000
F81I	39	-968.2074	2155.4690	0.0000	1.0000
JC69I	36	-976.8291	2155.8619	0.0000	1.0000
F81IG	40	-967.2431	2159.1571	0.0000	1.0000
JC69IG	37	-975.7976	2159.4157	0.0000	1.0000
JC69	35	-996.5148	2189.6166	0.0000	1.0000
F81	38	-988.2781	2189.9935	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/chr3_7252.phylip = 1 - 275;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7252.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/chr3_7252.phylip = 1 - 275;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7252.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/chr3_7252.phylip = 1 - 275;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7252.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

