
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:20 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/chr4_15987.phylip" (19 taxa, 636 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	-1499.6683	3084.8492	0.2729	0.2729
HKYI	40	-1499.9625	3085.4377	0.2033	0.4762
GTRG	44	-1495.4053	3085.5111	0.1960	0.6722
GTRI	44	-1495.6370	3085.9745	0.1555	0.8276
HKYIG	41	-1499.4870	3086.7719	0.1043	0.9319
GTRIG	45	-1495.3048	3087.6266	0.0681	1.0000
HKY	39	-1511.7416	3106.7181	0.0000	1.0000
GTR	43	-1507.5517	3107.4953	0.0000	1.0000
F81G	39	-1514.6724	3112.5797	0.0000	1.0000
F81I	39	-1514.8577	3112.9504	0.0000	1.0000
F81IG	40	-1514.6026	3114.7177	0.0000	1.0000
K2PG	37	-1520.1687	3119.0398	0.0000	1.0000
K2PI	37	-1520.4771	3119.6565	0.0000	1.0000
K2PIG	38	-1519.9773	3120.9194	0.0000	1.0000
SYMG	41	-1518.1744	3124.1468	0.0000	1.0000
SYMI	41	-1518.4470	3124.6920	0.0000	1.0000
SYMIG	42	-1518.0581	3126.2072	0.0000	1.0000
F81	38	-1526.1608	3133.2864	0.0000	1.0000
K2P	36	-1532.1545	3140.7564	0.0000	1.0000
JC69G	36	-1533.1054	3142.6582	0.0000	1.0000
JC69I	36	-1533.2981	3143.0436	0.0000	1.0000
JC69IG	37	-1533.0299	3144.7621	0.0000	1.0000
SYM	40	-1529.9959	3145.5045	0.0000	1.0000
JC69	35	-1544.6527	3163.5055	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1495.4053	3078.8106	0.2577	0.2577
GTRI	44	-1495.6370	3079.2740	0.2044	0.4621
HKYG	40	-1499.6683	3079.3366	0.1981	0.6602
HKYI	40	-1499.9625	3079.9251	0.1476	0.8078
GTRIG	45	-1495.3048	3080.6096	0.1048	0.9126
HKYIG	41	-1499.4870	3080.9740	0.0874	1.0000
GTR	43	-1507.5517	3101.1034	0.0000	1.0000
HKY	39	-1511.7416	3101.4832	0.0000	1.0000
F81G	39	-1514.6724	3107.3448	0.0000	1.0000
F81I	39	-1514.8577	3107.7155	0.0000	1.0000
F81IG	40	-1514.6026	3109.2051	0.0000	1.0000
K2PG	37	-1520.1687	3114.3374	0.0000	1.0000
K2PI	37	-1520.4771	3114.9542	0.0000	1.0000
K2PIG	38	-1519.9773	3115.9546	0.0000	1.0000
SYMG	41	-1518.1744	3118.3488	0.0000	1.0000
SYMI	41	-1518.4470	3118.8940	0.0000	1.0000
SYMIG	42	-1518.0581	3120.1161	0.0000	1.0000
F81	38	-1526.1608	3128.3216	0.0000	1.0000
K2P	36	-1532.1545	3136.3090	0.0000	1.0000
JC69G	36	-1533.1054	3138.2107	0.0000	1.0000
JC69I	36	-1533.2981	3138.5961	0.0000	1.0000
SYM	40	-1529.9959	3139.9919	0.0000	1.0000
JC69IG	37	-1533.0299	3140.0597	0.0000	1.0000
JC69	35	-1544.6527	3159.3055	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1499.6683	3257.5446	0.5577	0.5577
HKYI	40	-1499.9625	3258.1330	0.4155	0.9732
HKYIG	41	-1499.4870	3263.6371	0.0265	0.9997
GTRG	44	-1495.4053	3274.8393	0.0001	0.9998
HKY	39	-1511.7416	3275.2359	0.0001	0.9999
GTRI	44	-1495.6370	3275.3027	0.0001	1.0000
K2PG	37	-1520.1687	3279.1798	0.0000	1.0000
K2PI	37	-1520.4771	3279.7965	0.0000	1.0000
GTRIG	45	-1495.3048	3281.0936	0.0000	1.0000
F81G	39	-1514.6724	3281.0975	0.0000	1.0000
F81I	39	-1514.8577	3281.4682	0.0000	1.0000
K2PIG	38	-1519.9773	3285.2522	0.0000	1.0000
F81IG	40	-1514.6026	3287.4130	0.0000	1.0000
GTR	43	-1507.5517	3292.6769	0.0000	1.0000
K2P	36	-1532.1545	3296.6961	0.0000	1.0000
F81	38	-1526.1608	3297.6191	0.0000	1.0000
JC69G	36	-1533.1054	3298.5979	0.0000	1.0000
JC69I	36	-1533.2981	3298.9833	0.0000	1.0000
SYMG	41	-1518.1744	3301.0119	0.0000	1.0000
SYMI	41	-1518.4470	3301.5571	0.0000	1.0000
JC69IG	37	-1533.0299	3304.9021	0.0000	1.0000
SYMIG	42	-1518.0581	3307.2345	0.0000	1.0000
JC69	35	-1544.6527	3315.2374	0.0000	1.0000
SYM	40	-1529.9959	3318.1998	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/chr4_15987.phylip = 1 - 636;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_15987.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/chr4_15987.phylip = 1 - 636;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_15987.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/chr4_15987.phylip = 1 - 636;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_15987.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

