
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:44 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/chr21_1474.phylip" (19 taxa, 529 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	-2108.1993	4312.5803	0.6364	0.6364
GTRIG	45	-2107.7253	4314.0220	0.3095	0.9459
HKYG	40	-2116.1439	4319.0090	0.0256	0.9714
HKYIG	41	-2115.4801	4320.0320	0.0153	0.9868
K2PG	37	-2121.0572	4321.8415	0.0062	0.9930
K2PIG	38	-2120.3893	4322.8275	0.0038	0.9968
SYMG	41	-2117.7994	4324.6707	0.0015	0.9983
SYMIG	42	-2117.1086	4325.6494	0.0009	0.9992
HKYI	40	-2120.0716	4326.8645	0.0005	0.9997
GTRI	44	-2115.9886	4328.1590	0.0003	1.0000
SYMI	41	-2121.7709	4332.6137	0.0000	1.0000
K2PI	37	-2129.8575	4339.4421	0.0000	1.0000
GTR	43	-2171.9250	4437.6520	0.0000	1.0000
HKY	39	-2176.8928	4438.1659	0.0000	1.0000
F81G	39	-2177.0218	4438.4239	0.0000	1.0000
F81IG	40	-2176.5296	4439.7804	0.0000	1.0000
K2P	36	-2182.9574	4443.3295	0.0000	1.0000
SYM	40	-2178.5890	4443.8994	0.0000	1.0000
JC69G	36	-2186.3490	4450.1127	0.0000	1.0000
JC69IG	37	-2185.8530	4451.4331	0.0000	1.0000
F81I	39	-2185.2483	4454.8770	0.0000	1.0000
JC69I	36	-2194.4402	4466.2950	0.0000	1.0000
F81	38	-2236.2592	4554.5674	0.0000	1.0000
JC69	35	-2245.2491	4565.6097	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2108.1993	4304.3985	0.6127	0.6127
GTRIG	45	-2107.7253	4305.4505	0.3621	0.9747
HKYG	40	-2116.1439	4312.2877	0.0119	0.9866
HKYIG	41	-2115.4801	4312.9602	0.0085	0.9950
K2PG	37	-2121.0572	4316.1144	0.0018	0.9968
K2PIG	38	-2120.3893	4316.7785	0.0013	0.9981
SYMG	41	-2117.7994	4317.5989	0.0008	0.9989
SYMIG	42	-2117.1086	4318.2173	0.0006	0.9995
GTRI	44	-2115.9886	4319.9772	0.0003	0.9998
HKYI	40	-2120.0716	4320.1432	0.0002	1.0000
SYMI	41	-2121.7709	4325.5418	0.0000	1.0000
K2PI	37	-2129.8575	4333.7150	0.0000	1.0000
GTR	43	-2171.9250	4429.8499	0.0000	1.0000
HKY	39	-2176.8928	4431.7855	0.0000	1.0000
F81G	39	-2177.0218	4432.0435	0.0000	1.0000
F81IG	40	-2176.5296	4433.0591	0.0000	1.0000
SYM	40	-2178.5890	4437.1781	0.0000	1.0000
K2P	36	-2182.9574	4437.9149	0.0000	1.0000
JC69G	36	-2186.3490	4444.6981	0.0000	1.0000
JC69IG	37	-2185.8530	4445.7060	0.0000	1.0000
F81I	39	-2185.2483	4448.4966	0.0000	1.0000
JC69I	36	-2194.4402	4460.8803	0.0000	1.0000
F81	38	-2236.2592	4548.5184	0.0000	1.0000
JC69	35	-2245.2491	4560.4981	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2121.0572	4474.1410	0.9111	0.9111
K2PIG	38	-2120.3893	4479.0761	0.0773	0.9884
HKYG	40	-2116.1439	4483.1273	0.0102	0.9986
HKYIG	41	-2115.4801	4488.0707	0.0009	0.9995
HKYI	40	-2120.0716	4490.9828	0.0002	0.9997
K2PI	37	-2129.8575	4491.7416	0.0001	0.9998
GTRG	44	-2108.1993	4492.3220	0.0001	0.9999
SYMG	41	-2117.7994	4492.7094	0.0001	1.0000
SYMIG	42	-2117.1086	4497.5988	0.0000	1.0000
GTRIG	45	-2107.7253	4497.6450	0.0000	1.0000
SYMI	41	-2121.7709	4500.6524	0.0000	1.0000
GTRI	44	-2115.9886	4507.9007	0.0000	1.0000
K2P	36	-2182.9574	4591.6704	0.0000	1.0000
HKY	39	-2176.8928	4598.3541	0.0000	1.0000
JC69G	36	-2186.3490	4598.4536	0.0000	1.0000
F81G	39	-2177.0218	4598.6121	0.0000	1.0000
JC69IG	37	-2185.8530	4603.7326	0.0000	1.0000
F81IG	40	-2176.5296	4603.8986	0.0000	1.0000
SYM	40	-2178.5890	4608.0176	0.0000	1.0000
GTR	43	-2171.9250	4613.5024	0.0000	1.0000
JC69I	36	-2194.4402	4614.6359	0.0000	1.0000
F81I	39	-2185.2483	4615.0652	0.0000	1.0000
JC69	35	-2245.2491	4709.9827	0.0000	1.0000
F81	38	-2236.2592	4710.8160	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/chr21_1474.phylip = 1 - 529;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr21_1474.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/chr21_1474.phylip = 1 - 529;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr21_1474.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/chr21_1474.phylip = 1 - 529;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr21_1474.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

