
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:33 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_9696.phylip" (19 taxa, 347 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: HKYI


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
HKYI	40	-957.9585	2006.6359	0.4422	0.4422
HKYG	40	-958.1674	2007.0537	0.3588	0.8010
HKYIG	41	-957.9630	2009.2178	0.1216	0.9227
HKY	39	-961.6549	2011.4726	0.0394	0.9620
GTRI	44	-955.9296	2012.9717	0.0186	0.9807
GTRG	44	-956.2325	2013.5776	0.0137	0.9944
GTRIG	45	-955.9377	2015.6295	0.0049	0.9993
GTR	43	-960.5817	2019.6519	0.0007	1.0000
K2PI	37	-975.4635	2034.0274	0.0000	1.0000
K2PG	37	-975.5557	2034.2117	0.0000	1.0000
K2PIG	38	-975.4654	2036.5542	0.0000	1.0000
K2P	36	-978.2910	2037.1755	0.0000	1.0000
F81I	39	-977.0333	2042.2295	0.0000	1.0000
F81G	39	-977.1656	2042.4940	0.0000	1.0000
SYMI	41	-974.9199	2043.1316	0.0000	1.0000
SYMG	41	-974.9764	2043.2447	0.0000	1.0000
F81IG	40	-977.0363	2044.7916	0.0000	1.0000
F81	38	-979.9338	2045.4909	0.0000	1.0000
SYMIG	42	-974.9680	2045.8175	0.0000	1.0000
SYM	40	-977.8363	2046.3915	0.0000	1.0000
JC69I	36	-991.4802	2063.5539	0.0000	1.0000
JC69G	36	-991.5678	2063.7292	0.0000	1.0000
JC69IG	37	-991.5588	2066.2178	0.0000	1.0000
JC69	35	-994.1019	2066.3068	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-957.9585	1995.9170	0.3934	0.3934
HKYG	40	-958.1674	1996.3348	0.3193	0.7127
HKYIG	41	-957.9630	1997.9260	0.1441	0.8568
GTRI	44	-955.9296	1999.8592	0.0548	0.9116
GTRG	44	-956.2325	2000.4650	0.0405	0.9520
HKY	39	-961.6549	2001.3097	0.0265	0.9786
GTRIG	45	-955.9377	2001.8754	0.0200	0.9986
GTR	43	-960.5817	2007.1634	0.0014	1.0000
K2PI	37	-975.4635	2024.9270	0.0000	1.0000
K2PG	37	-975.5557	2025.1114	0.0000	1.0000
K2PIG	38	-975.4654	2026.9308	0.0000	1.0000
K2P	36	-978.2910	2028.5819	0.0000	1.0000
SYMI	41	-974.9199	2031.8398	0.0000	1.0000
SYMG	41	-974.9764	2031.9529	0.0000	1.0000
F81I	39	-977.0333	2032.0666	0.0000	1.0000
F81G	39	-977.1656	2032.3312	0.0000	1.0000
SYMIG	42	-974.9680	2033.9360	0.0000	1.0000
F81IG	40	-977.0363	2034.0727	0.0000	1.0000
SYM	40	-977.8363	2035.6726	0.0000	1.0000
F81	38	-979.9338	2035.8676	0.0000	1.0000
JC69I	36	-991.4802	2054.9604	0.0000	1.0000
JC69G	36	-991.5678	2055.1356	0.0000	1.0000
JC69IG	37	-991.5588	2057.1175	0.0000	1.0000
JC69	35	-994.1019	2058.2039	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-957.9585	2149.8900	0.4296	0.4296
HKYG	40	-958.1674	2150.3078	0.3486	0.7782
HKY	39	-961.6549	2151.4334	0.1986	0.9768
HKYIG	41	-957.9630	2155.7483	0.0230	0.9997
K2P	36	-978.2910	2167.1576	0.0001	0.9998
K2PI	37	-975.4635	2167.3521	0.0001	0.9999
K2PG	37	-975.5557	2167.5364	0.0001	0.9999
GTRI	44	-955.9296	2169.2295	0.0000	1.0000
GTRG	44	-956.2325	2169.8353	0.0000	1.0000
GTR	43	-960.5817	2172.6844	0.0000	1.0000
K2PIG	38	-975.4654	2173.2052	0.0000	1.0000
GTRIG	45	-955.9377	2175.0950	0.0000	1.0000
F81	38	-979.9338	2182.1419	0.0000	1.0000
F81I	39	-977.0333	2182.1903	0.0000	1.0000
F81G	39	-977.1656	2182.4548	0.0000	1.0000
F81IG	40	-977.0363	2188.0457	0.0000	1.0000
SYM	40	-977.8363	2189.6456	0.0000	1.0000
SYMI	41	-974.9199	2189.6621	0.0000	1.0000
SYMG	41	-974.9764	2189.7752	0.0000	1.0000
JC69	35	-994.1019	2192.9302	0.0000	1.0000
JC69I	36	-991.4802	2193.5361	0.0000	1.0000
JC69G	36	-991.5678	2193.7113	0.0000	1.0000
SYMIG	42	-974.9680	2195.6076	0.0000	1.0000
JC69IG	37	-991.5588	2199.5425	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9696.phylip = 1 - 347;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9696.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9696.phylip = 1 - 347;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9696.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9696.phylip = 1 - 347;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9696.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

