
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:32 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_31654.phylip" (19 taxa, 643 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
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
HKYIG	41	-1928.2619	3944.2542	0.5544	0.5544
HKYG	40	-1929.7663	3944.9811	0.3855	0.9399
HKYI	40	-1931.9937	3949.4359	0.0416	0.9815
GTRIG	45	-1927.5964	3952.1274	0.0108	0.9923
GTRG	44	-1929.1755	3952.9732	0.0071	0.9994
GTRI	44	-1931.6401	3957.9023	0.0006	1.0000
K2PIG	38	-1951.3237	3983.5547	0.0000	1.0000
K2PG	37	-1952.5988	3983.8455	0.0000	1.0000
K2PI	37	-1954.2751	3987.1982	0.0000	1.0000
SYMIG	42	-1950.1844	3990.3888	0.0000	1.0000
SYMG	41	-1951.5332	3990.7968	0.0000	1.0000
SYMI	41	-1953.3592	3994.4488	0.0000	1.0000
HKY	39	-1970.2496	4023.6733	0.0000	1.0000
GTR	43	-1969.2544	4030.8260	0.0000	1.0000
F81G	39	-1983.4339	4050.0420	0.0000	1.0000
F81IG	40	-1982.3876	4050.2238	0.0000	1.0000
F81I	39	-1985.2125	4053.5990	0.0000	1.0000
K2P	36	-1994.3703	4065.1366	0.0000	1.0000
SYM	40	-1992.6056	4070.6596	0.0000	1.0000
JC69G	36	-2003.0562	4082.5084	0.0000	1.0000
JC69IG	37	-2002.0538	4082.7556	0.0000	1.0000
JC69I	36	-2004.7334	4085.8629	0.0000	1.0000
F81	38	-2023.1667	4127.2407	0.0000	1.0000
JC69	35	-2042.3234	4158.7983	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-1928.2619	3938.5238	0.5793	0.5793
HKYG	40	-1929.7663	3939.5326	0.3498	0.9291
HKYI	40	-1931.9937	3943.9874	0.0377	0.9668
GTRIG	45	-1927.5964	3945.1928	0.0206	0.9874
GTRG	44	-1929.1755	3946.3511	0.0116	0.9990
GTRI	44	-1931.6401	3951.2802	0.0010	1.0000
K2PIG	38	-1951.3237	3978.6475	0.0000	1.0000
K2PG	37	-1952.5988	3979.1976	0.0000	1.0000
K2PI	37	-1954.2751	3982.5503	0.0000	1.0000
SYMIG	42	-1950.1844	3984.3688	0.0000	1.0000
SYMG	41	-1951.5332	3985.0663	0.0000	1.0000
SYMI	41	-1953.3592	3988.7184	0.0000	1.0000
HKY	39	-1970.2496	4018.4991	0.0000	1.0000
GTR	43	-1969.2544	4024.5088	0.0000	1.0000
F81IG	40	-1982.3876	4044.7753	0.0000	1.0000
F81G	39	-1983.4339	4044.8679	0.0000	1.0000
F81I	39	-1985.2125	4048.4249	0.0000	1.0000
K2P	36	-1994.3703	4060.7405	0.0000	1.0000
SYM	40	-1992.6056	4065.2111	0.0000	1.0000
JC69IG	37	-2002.0538	4078.1076	0.0000	1.0000
JC69G	36	-2003.0562	4078.1124	0.0000	1.0000
JC69I	36	-2004.7334	4081.4669	0.0000	1.0000
F81	38	-2023.1667	4122.3334	0.0000	1.0000
JC69	35	-2042.3234	4154.6468	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1929.7663	4118.1784	0.7780	0.7780
HKYIG	41	-1928.2619	4121.6357	0.1381	0.9161
HKYI	40	-1931.9937	4122.6331	0.0839	1.0000
GTRG	44	-1929.1755	4142.8615	0.0000	1.0000
K2PG	37	-1952.5988	4144.4449	0.0000	1.0000
GTRIG	45	-1927.5964	4146.1693	0.0000	1.0000
GTRI	44	-1931.6401	4147.7906	0.0000	1.0000
K2PI	37	-1954.2751	4147.7977	0.0000	1.0000
K2PIG	38	-1951.3237	4148.3610	0.0000	1.0000
SYMG	41	-1951.5332	4168.1783	0.0000	1.0000
SYMI	41	-1953.3592	4171.8303	0.0000	1.0000
SYMIG	42	-1950.1844	4171.9469	0.0000	1.0000
HKY	39	-1970.2496	4192.6788	0.0000	1.0000
GTR	43	-1969.2544	4216.5530	0.0000	1.0000
F81G	39	-1983.4339	4219.0475	0.0000	1.0000
K2P	36	-1994.3703	4221.5217	0.0000	1.0000
F81I	39	-1985.2125	4222.6046	0.0000	1.0000
F81IG	40	-1982.3876	4223.4211	0.0000	1.0000
JC69G	36	-2003.0562	4238.8936	0.0000	1.0000
JC69I	36	-2004.7334	4242.2481	0.0000	1.0000
JC69IG	37	-2002.0538	4243.3550	0.0000	1.0000
SYM	40	-1992.6056	4243.8569	0.0000	1.0000
F81	38	-2023.1667	4292.0469	0.0000	1.0000
JC69	35	-2042.3234	4310.9618	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31654.phylip = 1 - 643;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31654.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31654.phylip = 1 - 643;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31654.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) 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/chr1_31654.phylip = 1 - 643;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31654.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

