
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:08 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_5552.phylip" (19 taxa, 333 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
Minimum BIC  model: K2PG


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	-945.3535	1981.9398	0.3984	0.3984
HKYIG	41	-944.8747	1983.5844	0.1750	0.5734
GTRG	44	-941.0173	1983.7846	0.1584	0.7318
HKYI	40	-946.6014	1984.4358	0.1144	0.8461
GTRI	44	-941.6139	1984.9778	0.0872	0.9333
GTRIG	45	-940.7932	1986.0114	0.0520	0.9853
K2PG	37	-953.3772	1990.2867	0.0061	0.9915
K2PIG	38	-952.9009	1991.8834	0.0028	0.9942
SYMG	41	-949.2754	1992.3859	0.0021	0.9964
K2PI	37	-954.6288	1992.7897	0.0018	0.9981
SYMI	41	-949.9052	1993.6455	0.0011	0.9993
SYMIG	42	-949.0856	1994.6265	0.0007	1.0000
GTR	43	-952.4939	2004.0812	0.0000	1.0000
HKY	39	-958.1000	2004.8485	0.0000	1.0000
SYM	40	-960.5655	2012.3639	0.0000	1.0000
K2P	36	-966.5553	2014.1107	0.0000	1.0000
F81G	39	-977.3335	2043.3155	0.0000	1.0000
F81I	39	-977.8312	2044.3110	0.0000	1.0000
F81IG	40	-977.1311	2045.4950	0.0000	1.0000
JC69G	36	-984.0992	2049.1984	0.0000	1.0000
JC69I	36	-984.5872	2050.1743	0.0000	1.0000
JC69IG	37	-983.9038	2051.3398	0.0000	1.0000
F81	38	-988.8542	2063.7900	0.0000	1.0000
JC69	35	-995.5495	2069.5839	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-941.0173	1970.0346	0.2964	0.2964
HKYG	40	-945.3535	1970.7069	0.2118	0.5081
GTRI	44	-941.6139	1971.2278	0.1632	0.6714
GTRIG	45	-940.7932	1971.5864	0.1364	0.8078
HKYIG	41	-944.8747	1971.7494	0.1257	0.9335
HKYI	40	-946.6014	1973.2029	0.0608	0.9943
SYMG	41	-949.2754	1980.5508	0.0015	0.9959
K2PG	37	-953.3772	1980.7545	0.0014	0.9973
K2PIG	38	-952.9009	1981.8017	0.0008	0.9981
SYMI	41	-949.9052	1981.8105	0.0008	0.9989
SYMIG	42	-949.0856	1982.1713	0.0007	0.9996
K2PI	37	-954.6288	1983.2575	0.0004	1.0000
GTR	43	-952.4939	1990.9877	0.0000	1.0000
HKY	39	-958.1000	1994.2000	0.0000	1.0000
SYM	40	-960.5655	2001.1310	0.0000	1.0000
K2P	36	-966.5553	2005.1107	0.0000	1.0000
F81G	39	-977.3335	2032.6671	0.0000	1.0000
F81I	39	-977.8312	2033.6625	0.0000	1.0000
F81IG	40	-977.1311	2034.2621	0.0000	1.0000
JC69G	36	-984.0992	2040.1984	0.0000	1.0000
JC69I	36	-984.5872	2041.1743	0.0000	1.0000
JC69IG	37	-983.9038	2041.8076	0.0000	1.0000
F81	38	-988.8542	2053.7083	0.0000	1.0000
JC69	35	-995.5495	2061.0990	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-953.3772	2121.6557	0.4838	0.4838
HKYG	40	-945.3535	2123.0326	0.2431	0.7269
K2PI	37	-954.6288	2124.1588	0.1384	0.8653
HKYI	40	-946.6014	2125.5286	0.0698	0.9351
K2PIG	38	-952.9009	2126.5111	0.0427	0.9778
HKYIG	41	-944.8747	2127.8832	0.0215	0.9993
SYMG	41	-949.2754	2136.6847	0.0003	0.9995
GTRG	44	-941.0173	2137.5929	0.0002	0.9997
SYMI	41	-949.9052	2137.9443	0.0001	0.9998
GTRI	44	-941.6139	2138.7860	0.0001	0.9999
SYMIG	42	-949.0856	2142.1133	0.0000	1.0000
K2P	36	-966.5553	2142.2038	0.0000	1.0000
HKY	39	-958.1000	2142.7176	0.0000	1.0000
GTRIG	45	-940.7932	2142.9528	0.0000	1.0000
SYM	40	-960.5655	2153.4567	0.0000	1.0000
GTR	43	-952.4939	2154.7379	0.0000	1.0000
JC69G	36	-984.0992	2177.2915	0.0000	1.0000
JC69I	36	-984.5872	2178.2675	0.0000	1.0000
F81G	39	-977.3335	2181.1846	0.0000	1.0000
F81I	39	-977.8312	2182.1801	0.0000	1.0000
JC69IG	37	-983.9038	2182.7089	0.0000	1.0000
F81IG	40	-977.1311	2186.5878	0.0000	1.0000
JC69	35	-995.5495	2194.3840	0.0000	1.0000
F81	38	-988.8542	2198.4177	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_5552.phylip = 1 - 333;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5552.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_5552.phylip = 1 - 333;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5552.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5552.phylip = 1 - 333;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5552.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

