
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/chr3_5659.phylip" (19 taxa, 331 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1105.4978	2312.8417	0.5890	0.5890
GTRI	44	-1106.6402	2315.1265	0.1879	0.7769
GTRIG	45	-1105.4960	2315.5184	0.1545	0.9314
HKYG	40	-1113.4845	2318.2793	0.0388	0.9702
HKYI	40	-1114.3362	2319.9827	0.0166	0.9868
HKYIG	41	-1113.5698	2321.0565	0.0097	0.9965
K2PG	37	-1120.5829	2324.7631	0.0015	0.9980
K2PI	37	-1121.2810	2326.1593	0.0008	0.9988
SYMG	41	-1116.6766	2327.2702	0.0004	0.9992
K2PIG	38	-1120.5835	2327.3176	0.0004	0.9996
SYMI	41	-1117.3768	2328.6705	0.0002	0.9998
SYMIG	42	-1116.6095	2329.7606	0.0001	1.0000
GTR	43	-1116.7127	2332.6100	0.0000	1.0000
HKY	39	-1123.0597	2334.8410	0.0000	1.0000
K2P	36	-1129.7256	2340.5124	0.0000	1.0000
SYM	40	-1126.2118	2343.7339	0.0000	1.0000
F81G	39	-1142.8019	2374.3254	0.0000	1.0000
F81I	39	-1143.7701	2376.2619	0.0000	1.0000
JC69G	36	-1147.8344	2376.7301	0.0000	1.0000
F81IG	40	-1142.8012	2376.9127	0.0000	1.0000
JC69I	36	-1148.7829	2378.6271	0.0000	1.0000
JC69IG	37	-1147.8389	2379.2751	0.0000	1.0000
F81	38	-1151.0406	2388.2320	0.0000	1.0000
JC69	35	-1155.9067	2390.3558	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1105.4978	2298.9955	0.5809	0.5809
GTRIG	45	-1105.4960	2300.9921	0.2141	0.7950
GTRI	44	-1106.6402	2301.2804	0.1853	0.9803
HKYG	40	-1113.4845	2306.9689	0.0108	0.9911
HKYI	40	-1114.3362	2308.6723	0.0046	0.9957
HKYIG	41	-1113.5698	2309.1396	0.0036	0.9993
K2PG	37	-1120.5829	2315.1658	0.0002	0.9995
SYMG	41	-1116.6766	2315.3532	0.0002	0.9997
K2PI	37	-1121.2810	2316.5621	0.0001	0.9998
SYMI	41	-1117.3768	2316.7536	0.0001	0.9998
K2PIG	38	-1120.5835	2317.1669	0.0001	0.9999
SYMIG	42	-1116.6095	2317.2189	0.0001	1.0000
GTR	43	-1116.7127	2319.4253	0.0000	1.0000
HKY	39	-1123.0597	2324.1194	0.0000	1.0000
K2P	36	-1129.7256	2331.4512	0.0000	1.0000
SYM	40	-1126.2118	2332.4235	0.0000	1.0000
F81G	39	-1142.8019	2363.6037	0.0000	1.0000
F81I	39	-1143.7701	2365.5403	0.0000	1.0000
F81IG	40	-1142.8012	2365.6024	0.0000	1.0000
JC69G	36	-1147.8344	2367.6689	0.0000	1.0000
JC69I	36	-1148.7829	2369.5658	0.0000	1.0000
JC69IG	37	-1147.8389	2369.6778	0.0000	1.0000
F81	38	-1151.0406	2378.0813	0.0000	1.0000
JC69	35	-1155.9067	2381.8134	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1120.5829	2455.8442	0.5378	0.5378
K2PI	37	-1121.2810	2457.2404	0.2675	0.8053
HKYG	40	-1113.4845	2459.0537	0.1081	0.9133
HKYI	40	-1114.3362	2460.7571	0.0461	0.9595
K2PIG	38	-1120.5835	2461.6474	0.0295	0.9890
HKYIG	41	-1113.5698	2465.0264	0.0055	0.9944
GTRG	44	-1105.4978	2466.2887	0.0029	0.9974
K2P	36	-1129.7256	2468.3275	0.0010	0.9984
GTRI	44	-1106.6402	2468.5736	0.0009	0.9993
SYMG	41	-1116.6766	2471.2401	0.0002	0.9996
GTRIG	45	-1105.4960	2472.0874	0.0002	0.9997
HKY	39	-1123.0597	2472.4020	0.0001	0.9999
SYMI	41	-1117.3768	2472.6404	0.0001	1.0000
SYMIG	42	-1116.6095	2476.9079	0.0000	1.0000
GTR	43	-1116.7127	2482.9164	0.0000	1.0000
SYM	40	-1126.2118	2484.5083	0.0000	1.0000
JC69G	36	-1147.8344	2504.5451	0.0000	1.0000
JC69I	36	-1148.7829	2506.4421	0.0000	1.0000
JC69IG	37	-1147.8389	2510.3562	0.0000	1.0000
F81G	39	-1142.8019	2511.8864	0.0000	1.0000
F81I	39	-1143.7701	2513.8229	0.0000	1.0000
JC69	35	-1155.9067	2514.8876	0.0000	1.0000
F81IG	40	-1142.8012	2517.6871	0.0000	1.0000
F81	38	-1151.0406	2522.5618	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_5659.phylip = 1 - 331;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5659.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_5659.phylip = 1 - 331;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5659.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5659.phylip = 1 - 331;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5659.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

