
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:09 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/chr1_28729.phylip" (19 taxa, 651 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	-2180.7205	4455.9757	0.5835	0.5835
GTRI	44	-2181.6770	4457.8886	0.2242	0.8077
GTRIG	45	-2180.6883	4458.2196	0.1900	0.9977
HKYG	40	-2191.4453	4468.2676	0.0012	0.9990
HKYI	40	-2192.1325	4469.6421	0.0006	0.9996
HKYIG	41	-2191.4379	4470.5310	0.0004	1.0000
SYMG	41	-2198.5824	4484.8200	0.0000	1.0000
SYMI	41	-2199.1667	4485.9886	0.0000	1.0000
K2PG	37	-2203.9895	4486.5662	0.0000	1.0000
SYMIG	42	-2198.5804	4487.1016	0.0000	1.0000
K2PI	37	-2204.6770	4487.9413	0.0000	1.0000
K2PIG	38	-2203.9760	4488.7951	0.0000	1.0000
F81G	39	-2228.7816	4540.6697	0.0000	1.0000
F81I	39	-2229.2155	4541.5374	0.0000	1.0000
F81IG	40	-2228.7815	4542.9401	0.0000	1.0000
JC69G	36	-2238.8015	4553.9418	0.0000	1.0000
JC69I	36	-2239.2179	4554.7746	0.0000	1.0000
JC69IG	37	-2238.8023	4556.1919	0.0000	1.0000
GTR	43	-2240.3665	4572.9669	0.0000	1.0000
HKY	39	-2248.8118	4580.7300	0.0000	1.0000
SYM	40	-2256.2900	4597.9571	0.0000	1.0000
K2P	36	-2261.1598	4598.6584	0.0000	1.0000
F81	38	-2284.7914	4650.4260	0.0000	1.0000
JC69	35	-2294.9392	4663.9760	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2180.7205	4449.4410	0.5661	0.5661
GTRI	44	-2181.6770	4451.3539	0.2175	0.7836
GTRIG	45	-2180.6883	4451.3766	0.2151	0.9987
HKYG	40	-2191.4453	4462.8906	0.0007	0.9994
HKYI	40	-2192.1325	4464.2651	0.0003	0.9997
HKYIG	41	-2191.4379	4464.8758	0.0003	1.0000
SYMG	41	-2198.5824	4479.1648	0.0000	1.0000
SYMI	41	-2199.1667	4480.3334	0.0000	1.0000
SYMIG	42	-2198.5804	4481.1608	0.0000	1.0000
K2PG	37	-2203.9895	4481.9790	0.0000	1.0000
K2PI	37	-2204.6770	4483.3540	0.0000	1.0000
K2PIG	38	-2203.9760	4483.9520	0.0000	1.0000
F81G	39	-2228.7816	4535.5633	0.0000	1.0000
F81I	39	-2229.2155	4536.4310	0.0000	1.0000
F81IG	40	-2228.7815	4537.5630	0.0000	1.0000
JC69G	36	-2238.8015	4549.6031	0.0000	1.0000
JC69I	36	-2239.2179	4550.4358	0.0000	1.0000
JC69IG	37	-2238.8023	4551.6046	0.0000	1.0000
GTR	43	-2240.3665	4566.7330	0.0000	1.0000
HKY	39	-2248.8118	4575.6236	0.0000	1.0000
SYM	40	-2256.2900	4592.5800	0.0000	1.0000
K2P	36	-2261.1598	4594.3197	0.0000	1.0000
F81	38	-2284.7914	4645.5829	0.0000	1.0000
JC69	35	-2294.9392	4659.8785	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2191.4453	4642.0310	0.5597	0.5597
HKYI	40	-2192.1325	4643.4055	0.2815	0.8412
GTRG	44	-2180.7205	4646.4954	0.0600	0.9012
K2PG	37	-2203.9895	4647.6838	0.0331	0.9344
GTRI	44	-2181.6770	4648.4083	0.0231	0.9575
HKYIG	41	-2191.4379	4648.4947	0.0221	0.9796
K2PI	37	-2204.6770	4649.0589	0.0167	0.9962
GTRIG	45	-2180.6883	4652.9095	0.0024	0.9987
K2PIG	38	-2203.9760	4654.1354	0.0013	1.0000
SYMG	41	-2198.5824	4662.7837	0.0000	1.0000
SYMI	41	-2199.1667	4663.9523	0.0000	1.0000
SYMIG	42	-2198.5804	4669.2582	0.0000	1.0000
F81G	39	-2228.7816	4710.2252	0.0000	1.0000
JC69G	36	-2238.8015	4710.8294	0.0000	1.0000
F81I	39	-2229.2155	4711.0929	0.0000	1.0000
JC69I	36	-2239.2179	4711.6622	0.0000	1.0000
F81IG	40	-2228.7815	4716.7034	0.0000	1.0000
JC69IG	37	-2238.8023	4717.3094	0.0000	1.0000
HKY	39	-2248.8118	4750.2855	0.0000	1.0000
K2P	36	-2261.1598	4755.5460	0.0000	1.0000
GTR	43	-2240.3665	4759.3089	0.0000	1.0000
SYM	40	-2256.2900	4771.7204	0.0000	1.0000
F81	38	-2284.7914	4815.7662	0.0000	1.0000
JC69	35	-2294.9392	4816.6263	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/chr1_28729.phylip = 1 - 651;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28729.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/chr1_28729.phylip = 1 - 651;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28729.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/chr1_28729.phylip = 1 - 651;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28729.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

