
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:25 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/chr17_3013.phylip" (19 taxa, 924 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	-3143.3592	6379.2236	0.3749	0.3749
GTRIG	45	-3142.6927	6380.1007	0.2418	0.6166
HKYG	40	-3148.2352	6380.1851	0.2318	0.8484
HKYIG	41	-3147.5936	6381.0920	0.1473	0.9957
GTRI	44	-3148.2361	6388.9774	0.0029	0.9986
HKYI	40	-3153.3229	6390.3604	0.0014	1.0000
K2PG	37	-3164.8479	6406.8695	0.0000	1.0000
K2PIG	38	-3164.1896	6407.7283	0.0000	1.0000
SYMG	41	-3163.0764	6412.0575	0.0000	1.0000
SYMIG	42	-3162.4264	6412.9527	0.0000	1.0000
K2PI	37	-3170.4420	6418.0578	0.0000	1.0000
SYMI	41	-3168.1075	6422.1197	0.0000	1.0000
HKY	39	-3196.9833	6475.4961	0.0000	1.0000
GTR	43	-3193.5523	6477.4046	0.0000	1.0000
K2P	36	-3213.2016	6501.4067	0.0000	1.0000
SYM	40	-3211.2050	6506.1246	0.0000	1.0000
F81G	39	-3218.7216	6518.9725	0.0000	1.0000
F81IG	40	-3218.3023	6520.3193	0.0000	1.0000
F81I	39	-3223.8877	6529.3048	0.0000	1.0000
JC69G	36	-3232.6733	6540.3500	0.0000	1.0000
JC69IG	37	-3232.2466	6541.6670	0.0000	1.0000
JC69I	36	-3238.0403	6551.0839	0.0000	1.0000
F81	38	-3261.7611	6602.8713	0.0000	1.0000
JC69	35	-3275.6364	6624.1107	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3143.3592	6374.7185	0.4108	0.4108
GTRIG	45	-3142.6927	6375.3854	0.2943	0.7052
HKYG	40	-3148.2352	6376.4705	0.1711	0.8763
HKYIG	41	-3147.5936	6377.1873	0.1196	0.9958
GTRI	44	-3148.2361	6384.4723	0.0031	0.9989
HKYI	40	-3153.3229	6386.6458	0.0011	1.0000
K2PG	37	-3164.8479	6403.6957	0.0000	1.0000
K2PIG	38	-3164.1896	6404.3791	0.0000	1.0000
SYMG	41	-3163.0764	6408.1527	0.0000	1.0000
SYMIG	42	-3162.4264	6408.8528	0.0000	1.0000
K2PI	37	-3170.4420	6414.8840	0.0000	1.0000
SYMI	41	-3168.1075	6418.2149	0.0000	1.0000
HKY	39	-3196.9833	6471.9667	0.0000	1.0000
GTR	43	-3193.5523	6473.1046	0.0000	1.0000
K2P	36	-3213.2016	6498.4033	0.0000	1.0000
SYM	40	-3211.2050	6502.4100	0.0000	1.0000
F81G	39	-3218.7216	6515.4431	0.0000	1.0000
F81IG	40	-3218.3023	6516.6047	0.0000	1.0000
F81I	39	-3223.8877	6525.7754	0.0000	1.0000
JC69G	36	-3232.6733	6537.3467	0.0000	1.0000
JC69IG	37	-3232.2466	6538.4931	0.0000	1.0000
JC69I	36	-3238.0403	6548.0805	0.0000	1.0000
F81	38	-3261.7611	6599.5222	0.0000	1.0000
JC69	35	-3275.6364	6621.2728	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3148.2352	6569.6190	0.9340	0.9340
HKYIG	41	-3147.5936	6575.1645	0.0584	0.9924
HKYI	40	-3153.3229	6579.7942	0.0058	0.9981
K2PG	37	-3164.8479	6582.3580	0.0016	0.9997
GTRG	44	-3143.3592	6587.1818	0.0001	0.9999
K2PIG	38	-3164.1896	6587.8702	0.0001	1.0000
GTRIG	45	-3142.6927	6592.6775	0.0000	1.0000
K2PI	37	-3170.4420	6593.5463	0.0000	1.0000
GTRI	44	-3148.2361	6596.9356	0.0000	1.0000
SYMG	41	-3163.0764	6606.1299	0.0000	1.0000
SYMIG	42	-3162.4264	6611.6587	0.0000	1.0000
SYMI	41	-3168.1075	6616.1921	0.0000	1.0000
HKY	39	-3196.9833	6660.2865	0.0000	1.0000
K2P	36	-3213.2016	6672.2369	0.0000	1.0000
GTR	43	-3193.5523	6680.7392	0.0000	1.0000
SYM	40	-3211.2050	6695.5585	0.0000	1.0000
F81G	39	-3218.7216	6703.7629	0.0000	1.0000
F81IG	40	-3218.3023	6709.7532	0.0000	1.0000
JC69G	36	-3232.6733	6711.1803	0.0000	1.0000
F81I	39	-3223.8877	6714.0951	0.0000	1.0000
JC69IG	37	-3232.2466	6717.1555	0.0000	1.0000
JC69I	36	-3238.0403	6721.9141	0.0000	1.0000
F81	38	-3261.7611	6783.0132	0.0000	1.0000
JC69	35	-3275.6364	6790.2777	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/chr17_3013.phylip = 1 - 924;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3013.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/chr17_3013.phylip = 1 - 924;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3013.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/chr17_3013.phylip = 1 - 924;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3013.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

