
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:49 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/chr7_10353.phylip" (19 taxa, 367 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-949.1055	1998.5090	0.4902	0.4902
GTRI	44	-949.5148	1999.3277	0.3255	0.8157
GTRIG	45	-948.8799	2000.6569	0.1675	0.9832
HKYI	40	-958.4315	2006.9243	0.0073	0.9905
HKYG	40	-958.5043	2007.0699	0.0068	0.9972
HKYIG	41	-958.1429	2008.8828	0.0027	1.0000
GTR	43	-961.1265	2019.9683	0.0000	1.0000
F81I	39	-968.6894	2024.9201	0.0000	1.0000
F81G	39	-968.8389	2025.2192	0.0000	1.0000
HKY	39	-968.9453	2025.4319	0.0000	1.0000
F81IG	40	-968.8388	2027.7390	0.0000	1.0000
F81	38	-979.8798	2044.7963	0.0000	1.0000
SYMG	41	-981.1042	2054.8053	0.0000	1.0000
SYMI	41	-981.4230	2055.4430	0.0000	1.0000
K2PG	37	-986.8990	2056.3452	0.0000	1.0000
K2PI	37	-987.0383	2056.6236	0.0000	1.0000
SYMIG	42	-980.8318	2056.8117	0.0000	1.0000
K2PIG	38	-986.5113	2058.0592	0.0000	1.0000
JC69G	36	-993.3459	2066.7645	0.0000	1.0000
JC69I	36	-994.9814	2070.0355	0.0000	1.0000
JC69IG	37	-994.6334	2071.8139	0.0000	1.0000
SYM	40	-994.0598	2078.1809	0.0000	1.0000
K2P	36	-999.6225	2079.3178	0.0000	1.0000
JC69	35	-1005.0896	2087.7924	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-949.1055	1986.2109	0.4680	0.4680
GTRI	44	-949.5148	1987.0296	0.3108	0.7788
GTRIG	45	-948.8799	1987.7597	0.2157	0.9945
HKYI	40	-958.4315	1996.8630	0.0023	0.9968
HKYG	40	-958.5043	1997.0086	0.0021	0.9989
HKYIG	41	-958.1429	1998.2858	0.0011	1.0000
GTR	43	-961.1265	2008.2531	0.0000	1.0000
F81I	39	-968.6894	2015.3788	0.0000	1.0000
F81G	39	-968.8389	2015.6779	0.0000	1.0000
HKY	39	-968.9453	2015.8906	0.0000	1.0000
F81IG	40	-968.8388	2017.6777	0.0000	1.0000
F81	38	-979.8798	2035.7597	0.0000	1.0000
SYMG	41	-981.1042	2044.2084	0.0000	1.0000
SYMI	41	-981.4230	2044.8461	0.0000	1.0000
SYMIG	42	-980.8318	2045.6636	0.0000	1.0000
K2PG	37	-986.8990	2047.7981	0.0000	1.0000
K2PI	37	-987.0383	2048.0765	0.0000	1.0000
K2PIG	38	-986.5113	2049.0226	0.0000	1.0000
JC69G	36	-993.3459	2058.6917	0.0000	1.0000
JC69I	36	-994.9814	2061.9628	0.0000	1.0000
JC69IG	37	-994.6334	2063.2667	0.0000	1.0000
SYM	40	-994.0598	2068.1196	0.0000	1.0000
K2P	36	-999.6225	2071.2450	0.0000	1.0000
JC69	35	-1005.0896	2080.1791	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-958.4315	2153.0775	0.4661	0.4661
HKYG	40	-958.5043	2153.2230	0.4334	0.8995
GTRG	44	-949.1055	2158.0468	0.0389	0.9383
HKYIG	41	-958.1429	2158.4057	0.0325	0.9708
GTRI	44	-949.5148	2158.8655	0.0258	0.9966
GTRIG	45	-948.8799	2163.5010	0.0025	0.9992
F81I	39	-968.6894	2167.6879	0.0003	0.9995
F81G	39	-968.8389	2167.9870	0.0003	0.9997
HKY	39	-968.9453	2168.1997	0.0002	1.0000
F81IG	40	-968.8388	2173.8921	0.0000	1.0000
GTR	43	-961.1265	2176.1836	0.0000	1.0000
F81	38	-979.8798	2184.1634	0.0000	1.0000
K2PG	37	-986.8990	2192.2965	0.0000	1.0000
K2PI	37	-987.0383	2192.5749	0.0000	1.0000
K2PIG	38	-986.5113	2197.4264	0.0000	1.0000
JC69G	36	-993.3459	2199.2848	0.0000	1.0000
JC69I	36	-994.9814	2202.5558	0.0000	1.0000
SYMG	41	-981.1042	2204.3282	0.0000	1.0000
SYMI	41	-981.4230	2204.9659	0.0000	1.0000
JC69IG	37	-994.6334	2207.7651	0.0000	1.0000
SYMIG	42	-980.8318	2209.6888	0.0000	1.0000
K2P	36	-999.6225	2211.8381	0.0000	1.0000
JC69	35	-1005.0896	2216.8668	0.0000	1.0000
SYM	40	-994.0598	2224.3341	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/chr7_10353.phylip = 1 - 367;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10353.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/chr7_10353.phylip = 1 - 367;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10353.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 (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10353.phylip = 1 - 367;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10353.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

