
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:50 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_17498.phylip" (19 taxa, 694 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	-2107.8864	4309.8746	0.3541	0.3541
HKYG	40	-2112.9550	4310.9330	0.2086	0.5627
GTRI	44	-2108.6688	4311.4393	0.1619	0.7246
GTRIG	45	-2107.8143	4312.0174	0.1213	0.8459
HKYIG	41	-2112.7534	4312.7890	0.0825	0.9284
HKYI	40	-2114.0240	4313.0710	0.0716	1.0000
K2PG	37	-2136.0049	4350.2965	0.0000	1.0000
K2PIG	38	-2135.6811	4351.8875	0.0000	1.0000
K2PI	37	-2137.2790	4352.8446	0.0000	1.0000
SYMG	41	-2133.4522	4354.1866	0.0000	1.0000
SYMIG	42	-2133.2283	4356.0049	0.0000	1.0000
SYMI	41	-2134.5039	4356.2901	0.0000	1.0000
GTR	43	-2144.6263	4381.0742	0.0000	1.0000
HKY	39	-2149.7879	4382.3465	0.0000	1.0000
K2P	36	-2172.5989	4421.2526	0.0000	1.0000
SYM	40	-2169.6327	4424.2883	0.0000	1.0000
F81G	39	-2177.9272	4438.6251	0.0000	1.0000
F81IG	40	-2177.6727	4440.3684	0.0000	1.0000
F81I	39	-2179.0217	4440.8140	0.0000	1.0000
JC69G	36	-2195.4087	4466.8722	0.0000	1.0000
JC69IG	37	-2195.1034	4468.4933	0.0000	1.0000
JC69I	36	-2196.5826	4469.2199	0.0000	1.0000
F81	38	-2213.1209	4506.7671	0.0000	1.0000
JC69	35	-2230.9486	4535.7269	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2107.8864	4303.7729	0.4051	0.4051
GTRI	44	-2108.6688	4305.3376	0.1852	0.5903
GTRIG	45	-2107.8143	4305.6286	0.1602	0.7505
HKYG	40	-2112.9550	4305.9100	0.1391	0.8896
HKYIG	41	-2112.7534	4307.5068	0.0626	0.9522
HKYI	40	-2114.0240	4308.0480	0.0478	1.0000
K2PG	37	-2136.0049	4346.0099	0.0000	1.0000
K2PIG	38	-2135.6811	4347.3623	0.0000	1.0000
K2PI	37	-2137.2790	4348.5580	0.0000	1.0000
SYMG	41	-2133.4522	4348.9044	0.0000	1.0000
SYMIG	42	-2133.2283	4350.4565	0.0000	1.0000
SYMI	41	-2134.5039	4351.0079	0.0000	1.0000
GTR	43	-2144.6263	4375.2526	0.0000	1.0000
HKY	39	-2149.7879	4377.5759	0.0000	1.0000
K2P	36	-2172.5989	4417.1978	0.0000	1.0000
SYM	40	-2169.6327	4419.2653	0.0000	1.0000
F81G	39	-2177.9272	4433.8545	0.0000	1.0000
F81IG	40	-2177.6727	4435.3454	0.0000	1.0000
F81I	39	-2179.0217	4436.0434	0.0000	1.0000
JC69G	36	-2195.4087	4462.8174	0.0000	1.0000
JC69IG	37	-2195.1034	4464.2067	0.0000	1.0000
JC69I	36	-2196.5826	4465.1651	0.0000	1.0000
F81	38	-2213.1209	4502.2419	0.0000	1.0000
JC69	35	-2230.9486	4531.8971	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2112.9550	4487.6089	0.7193	0.7193
HKYI	40	-2114.0240	4489.7469	0.2470	0.9662
HKYIG	41	-2112.7534	4493.7482	0.0334	0.9996
GTRG	44	-2107.8864	4503.6416	0.0002	0.9999
GTRI	44	-2108.6688	4505.2064	0.0001	1.0000
GTRIG	45	-2107.8143	4510.0398	0.0000	1.0000
K2PG	37	-2136.0049	4514.0813	0.0000	1.0000
K2PI	37	-2137.2790	4516.6295	0.0000	1.0000
K2PIG	38	-2135.6811	4519.9762	0.0000	1.0000
SYMG	41	-2133.4522	4535.1458	0.0000	1.0000
SYMI	41	-2134.5039	4537.2492	0.0000	1.0000
SYMIG	42	-2133.2283	4541.2403	0.0000	1.0000
HKY	39	-2149.7879	4554.7323	0.0000	1.0000
GTR	43	-2144.6263	4570.5789	0.0000	1.0000
K2P	36	-2172.5989	4580.7268	0.0000	1.0000
SYM	40	-2169.6327	4600.9642	0.0000	1.0000
F81G	39	-2177.9272	4611.0109	0.0000	1.0000
F81I	39	-2179.0217	4613.1998	0.0000	1.0000
F81IG	40	-2177.6727	4617.0443	0.0000	1.0000
JC69G	36	-2195.4087	4626.3464	0.0000	1.0000
JC69I	36	-2196.5826	4628.6941	0.0000	1.0000
JC69IG	37	-2195.1034	4632.2782	0.0000	1.0000
F81	38	-2213.1209	4674.8558	0.0000	1.0000
JC69	35	-2230.9486	4690.8837	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_17498.phylip = 1 - 694;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17498.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_17498.phylip = 1 - 694;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17498.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_17498.phylip = 1 - 694;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17498.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

