
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:09 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/chr2_6737.phylip" (19 taxa, 317 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	-1022.1104	2136.1048	0.3405	0.3405
GTRG	44	-1016.8379	2136.2347	0.3191	0.6596
HKYI	40	-1023.3293	2138.5427	0.1006	0.7602
HKYIG	41	-1022.1144	2138.7524	0.0906	0.8508
GTRIG	45	-1016.8374	2138.9515	0.0820	0.9329
GTRI	44	-1018.4313	2139.4215	0.0648	0.9977
HKY	39	-1028.9025	2147.0685	0.0014	0.9991
GTR	43	-1024.0783	2148.0173	0.0009	1.0000
K2PG	37	-1041.7124	2167.5036	0.0000	1.0000
K2PI	37	-1042.4151	2168.9091	0.0000	1.0000
K2PIG	38	-1041.7032	2170.0683	0.0000	1.0000
SYMG	41	-1038.5847	2171.6931	0.0000	1.0000
SYMI	41	-1039.5278	2173.5793	0.0000	1.0000
SYMIG	42	-1038.5821	2174.3467	0.0000	1.0000
K2P	36	-1048.1506	2177.8155	0.0000	1.0000
SYM	40	-1045.1604	2182.2049	0.0000	1.0000
F81G	39	-1047.4461	2184.1557	0.0000	1.0000
F81I	39	-1048.6419	2186.5474	0.0000	1.0000
F81IG	40	-1047.4511	2186.7863	0.0000	1.0000
F81	38	-1053.5074	2193.6767	0.0000	1.0000
JC69G	36	-1062.9372	2207.3886	0.0000	1.0000
JC69I	36	-1064.1304	2209.7751	0.0000	1.0000
JC69IG	37	-1062.9427	2209.9642	0.0000	1.0000
JC69	35	-1068.8895	2216.7469	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1016.8379	2121.6759	0.4903	0.4903
GTRIG	45	-1016.8374	2123.6747	0.1805	0.6707
HKYG	40	-1022.1104	2124.2207	0.1373	0.8081
GTRI	44	-1018.4313	2124.8627	0.0996	0.9077
HKYIG	41	-1022.1144	2126.2288	0.0503	0.9580
HKYI	40	-1023.3293	2126.6586	0.0406	0.9986
GTR	43	-1024.0783	2134.1565	0.0010	0.9996
HKY	39	-1028.9025	2135.8049	0.0004	1.0000
K2PG	37	-1041.7124	2157.4247	0.0000	1.0000
K2PI	37	-1042.4151	2158.8303	0.0000	1.0000
SYMG	41	-1038.5847	2159.1695	0.0000	1.0000
K2PIG	38	-1041.7032	2159.4064	0.0000	1.0000
SYMI	41	-1039.5278	2161.0557	0.0000	1.0000
SYMIG	42	-1038.5821	2161.1643	0.0000	1.0000
K2P	36	-1048.1506	2168.3012	0.0000	1.0000
SYM	40	-1045.1604	2170.3208	0.0000	1.0000
F81G	39	-1047.4461	2172.8921	0.0000	1.0000
F81IG	40	-1047.4511	2174.9023	0.0000	1.0000
F81I	39	-1048.6419	2175.2838	0.0000	1.0000
F81	38	-1053.5074	2183.0148	0.0000	1.0000
JC69G	36	-1062.9372	2197.8743	0.0000	1.0000
JC69IG	37	-1062.9427	2199.8853	0.0000	1.0000
JC69I	36	-1064.1304	2200.2608	0.0000	1.0000
JC69	35	-1068.8895	2207.7789	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1022.1104	2274.5768	0.7278	0.7278
HKYI	40	-1023.3293	2277.0147	0.2151	0.9429
HKYIG	41	-1022.1144	2280.3437	0.0407	0.9836
HKY	39	-1028.9025	2282.4021	0.0145	0.9982
GTRG	44	-1016.8379	2287.0675	0.0014	0.9996
GTRI	44	-1018.4313	2290.2543	0.0003	0.9999
GTRIG	45	-1016.8374	2292.8253	0.0001	1.0000
GTR	43	-1024.0783	2295.7893	0.0000	1.0000
K2PG	37	-1041.7124	2296.5041	0.0000	1.0000
K2PI	37	-1042.4151	2297.9096	0.0000	1.0000
K2PIG	38	-1041.7032	2302.2446	0.0000	1.0000
K2P	36	-1048.1506	2303.6217	0.0000	1.0000
SYMG	41	-1038.5847	2313.2845	0.0000	1.0000
SYMI	41	-1039.5278	2315.1707	0.0000	1.0000
SYMIG	42	-1038.5821	2319.0381	0.0000	1.0000
F81G	39	-1047.4461	2319.4893	0.0000	1.0000
SYM	40	-1045.1604	2320.6769	0.0000	1.0000
F81I	39	-1048.6419	2321.8810	0.0000	1.0000
F81IG	40	-1047.4511	2325.2583	0.0000	1.0000
F81	38	-1053.5074	2325.8531	0.0000	1.0000
JC69G	36	-1062.9372	2333.1948	0.0000	1.0000
JC69I	36	-1064.1304	2335.5813	0.0000	1.0000
JC69IG	37	-1062.9427	2338.9647	0.0000	1.0000
JC69	35	-1068.8895	2339.3405	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/chr2_6737.phylip = 1 - 317;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_6737.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/chr2_6737.phylip = 1 - 317;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_6737.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/chr2_6737.phylip = 1 - 317;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_6737.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

