
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:57 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_3016.phylip" (19 taxa, 354 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1015.9280	2132.6716	0.4773	0.4773
GTRI	44	-1016.2675	2133.3504	0.3399	0.8172
GTRIG	45	-1015.9049	2135.2513	0.1314	0.9486
HKYG	40	-1024.1380	2138.7553	0.0228	0.9714
HKYI	40	-1024.1739	2138.8270	0.0220	0.9934
HKYIG	41	-1024.1454	2141.3292	0.0063	0.9997
GTR	43	-1024.7829	2147.7722	0.0003	1.0000
HKY	39	-1032.5376	2153.0116	0.0000	1.0000
K2PI	37	-1035.8222	2154.5432	0.0000	1.0000
K2PG	37	-1035.8910	2154.6808	0.0000	1.0000
SYMG	41	-1031.8851	2156.8087	0.0000	1.0000
SYMI	41	-1031.9178	2156.8740	0.0000	1.0000
K2PIG	38	-1035.9045	2157.2186	0.0000	1.0000
SYMIG	42	-1031.8839	2159.3820	0.0000	1.0000
K2P	36	-1044.4207	2169.2452	0.0000	1.0000
SYM	40	-1039.9724	2170.4241	0.0000	1.0000
F81I	39	-1046.8429	2181.6222	0.0000	1.0000
F81G	39	-1046.9382	2181.8128	0.0000	1.0000
F81IG	40	-1046.8290	2184.1373	0.0000	1.0000
JC69I	36	-1056.3341	2193.0720	0.0000	1.0000
JC69G	36	-1056.4715	2193.3467	0.0000	1.0000
F81	38	-1054.7260	2194.8616	0.0000	1.0000
JC69IG	37	-1056.3292	2195.5571	0.0000	1.0000
JC69	35	-1064.3870	2206.6984	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1015.9280	2119.8561	0.4709	0.4709
GTRI	44	-1016.2675	2120.5349	0.3354	0.8062
GTRIG	45	-1015.9049	2121.8097	0.1773	0.9835
HKYG	40	-1024.1380	2128.2761	0.0070	0.9905
HKYI	40	-1024.1739	2128.3478	0.0067	0.9973
HKYIG	41	-1024.1454	2130.2907	0.0026	0.9998
GTR	43	-1024.7829	2135.5657	0.0002	1.0000
HKY	39	-1032.5376	2143.0753	0.0000	1.0000
K2PI	37	-1035.8222	2145.6445	0.0000	1.0000
SYMG	41	-1031.8851	2145.7702	0.0000	1.0000
K2PG	37	-1035.8910	2145.7820	0.0000	1.0000
SYMI	41	-1031.9178	2145.8355	0.0000	1.0000
SYMIG	42	-1031.8839	2147.7678	0.0000	1.0000
K2PIG	38	-1035.9045	2147.8091	0.0000	1.0000
SYM	40	-1039.9724	2159.9448	0.0000	1.0000
K2P	36	-1044.4207	2160.8414	0.0000	1.0000
F81I	39	-1046.8429	2171.6859	0.0000	1.0000
F81G	39	-1046.9382	2171.8765	0.0000	1.0000
F81IG	40	-1046.8290	2173.6580	0.0000	1.0000
JC69I	36	-1056.3341	2184.6682	0.0000	1.0000
JC69G	36	-1056.4715	2184.9430	0.0000	1.0000
F81	38	-1054.7260	2185.4521	0.0000	1.0000
JC69IG	37	-1056.3292	2186.6583	0.0000	1.0000
JC69	35	-1064.3870	2198.7739	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1024.1380	2283.0479	0.4576	0.4576
HKYI	40	-1024.1739	2283.1197	0.4415	0.8991
K2PI	37	-1035.8222	2288.8085	0.0257	0.9248
HKYIG	41	-1024.1454	2288.9319	0.0241	0.9490
K2PG	37	-1035.8910	2288.9460	0.0240	0.9729
GTRG	44	-1015.9280	2290.1051	0.0134	0.9864
GTRI	44	-1016.2675	2290.7840	0.0096	0.9959
HKY	39	-1032.5376	2293.9778	0.0019	0.9979
K2PIG	38	-1035.9045	2294.8424	0.0013	0.9991
GTRIG	45	-1015.9049	2295.9281	0.0007	0.9999
K2P	36	-1044.4207	2300.1361	0.0001	0.9999
GTR	43	-1024.7829	2301.9455	0.0000	1.0000
SYMG	41	-1031.8851	2304.4114	0.0000	1.0000
SYMI	41	-1031.9178	2304.4767	0.0000	1.0000
SYMIG	42	-1031.8839	2310.2783	0.0000	1.0000
SYM	40	-1039.9724	2314.7167	0.0000	1.0000
F81I	39	-1046.8429	2322.5885	0.0000	1.0000
F81G	39	-1046.9382	2322.7791	0.0000	1.0000
JC69I	36	-1056.3341	2323.9629	0.0000	1.0000
JC69G	36	-1056.4715	2324.2376	0.0000	1.0000
F81IG	40	-1046.8290	2328.4299	0.0000	1.0000
JC69IG	37	-1056.3292	2329.8223	0.0000	1.0000
F81	38	-1054.7260	2332.4854	0.0000	1.0000
JC69	35	-1064.3870	2334.1993	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_3016.phylip = 1 - 354;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3016.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/chr3_3016.phylip = 1 - 354;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3016.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3016.phylip = 1 - 354;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3016.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

