
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:18 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/chr5_10904.phylip" (19 taxa, 1122 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-3626.3111	7346.4699	0.6286	0.6286
GTRG	44	-3628.5818	7348.8405	0.1921	0.8207
GTRI	44	-3628.7148	7349.1064	0.1682	0.9889
HKYG	40	-3636.2272	7355.4886	0.0069	0.9958
HKYIG	41	-3636.2073	7357.6035	0.0024	0.9982
HKYI	40	-3637.5823	7358.1988	0.0018	1.0000
GTR	43	-3653.0237	7395.5575	0.0000	1.0000
HKY	39	-3660.0307	7400.9449	0.0000	1.0000
F81IG	40	-3722.7808	7528.5958	0.0000	1.0000
F81G	39	-3724.0032	7528.8898	0.0000	1.0000
F81I	39	-3726.5844	7534.0524	0.0000	1.0000
K2PIG	38	-3728.4924	7535.7216	0.0000	1.0000
K2PI	37	-3731.4564	7539.5069	0.0000	1.0000
K2PG	37	-3731.5894	7539.7730	0.0000	1.0000
SYMIG	42	-3727.3643	7542.0761	0.0000	1.0000
SYMI	41	-3730.1235	7545.4359	0.0000	1.0000
SYMG	41	-3730.4703	7546.1294	0.0000	1.0000
F81	38	-3745.2955	7569.3279	0.0000	1.0000
K2P	36	-3757.1859	7588.8271	0.0000	1.0000
SYM	40	-3756.0141	7595.0625	0.0000	1.0000
JC69IG	37	-3796.9219	7670.4379	0.0000	1.0000
JC69G	36	-3801.0126	7676.4805	0.0000	1.0000
JC69I	36	-3803.7871	7682.0294	0.0000	1.0000
JC69	35	-3823.4601	7719.2406	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-3626.3111	7342.6223	0.6501	0.6501
GTRG	44	-3628.5818	7345.1636	0.1824	0.8325
GTRI	44	-3628.7148	7345.4295	0.1597	0.9922
HKYG	40	-3636.2272	7352.4544	0.0048	0.9970
HKYIG	41	-3636.2073	7354.4146	0.0018	0.9988
HKYI	40	-3637.5823	7355.1646	0.0012	1.0000
GTR	43	-3653.0237	7392.0473	0.0000	1.0000
HKY	39	-3660.0307	7398.0614	0.0000	1.0000
F81IG	40	-3722.7808	7525.5615	0.0000	1.0000
F81G	39	-3724.0032	7526.0063	0.0000	1.0000
F81I	39	-3726.5844	7531.1689	0.0000	1.0000
K2PIG	38	-3728.4924	7532.9848	0.0000	1.0000
K2PI	37	-3731.4564	7536.9128	0.0000	1.0000
K2PG	37	-3731.5894	7537.1789	0.0000	1.0000
SYMIG	42	-3727.3643	7538.7285	0.0000	1.0000
SYMI	41	-3730.1235	7542.2470	0.0000	1.0000
SYMG	41	-3730.4703	7542.9405	0.0000	1.0000
F81	38	-3745.2955	7566.5911	0.0000	1.0000
K2P	36	-3757.1859	7586.3718	0.0000	1.0000
SYM	40	-3756.0141	7592.0282	0.0000	1.0000
JC69IG	37	-3796.9219	7667.8438	0.0000	1.0000
JC69G	36	-3801.0126	7674.0252	0.0000	1.0000
JC69I	36	-3803.7871	7679.5741	0.0000	1.0000
JC69	35	-3823.4601	7716.9202	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3636.2272	7553.3691	0.7740	0.7740
HKYI	40	-3637.5823	7556.0793	0.1996	0.9736
HKYIG	41	-3636.2073	7560.3522	0.0236	0.9972
GTRG	44	-3628.5818	7566.1698	0.0013	0.9985
GTRI	44	-3628.7148	7566.4357	0.0011	0.9996
GTRIG	45	-3626.3111	7568.6514	0.0004	1.0000
HKY	39	-3660.0307	7593.9532	0.0000	1.0000
GTR	43	-3653.0237	7608.0307	0.0000	1.0000
F81G	39	-3724.0032	7721.8982	0.0000	1.0000
K2PI	37	-3731.4564	7722.7590	0.0000	1.0000
K2PG	37	-3731.5894	7723.0250	0.0000	1.0000
K2PIG	38	-3728.4924	7723.8538	0.0000	1.0000
F81IG	40	-3722.7808	7726.4763	0.0000	1.0000
F81I	39	-3726.5844	7727.0608	0.0000	1.0000
SYMI	41	-3730.1235	7748.1846	0.0000	1.0000
SYMG	41	-3730.4703	7748.8781	0.0000	1.0000
SYMIG	42	-3727.3643	7749.6890	0.0000	1.0000
F81	38	-3745.2955	7757.4600	0.0000	1.0000
K2P	36	-3757.1859	7767.1951	0.0000	1.0000
SYM	40	-3756.0141	7792.9430	0.0000	1.0000
JC69IG	37	-3796.9219	7853.6899	0.0000	1.0000
JC69G	36	-3801.0126	7854.8485	0.0000	1.0000
JC69I	36	-3803.7871	7860.3974	0.0000	1.0000
JC69	35	-3823.4601	7892.7206	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10904.phylip = 1 - 1122;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10904.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10904.phylip = 1 - 1122;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10904.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr5_10904.phylip = 1 - 1122;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10904.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

