
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:03 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/chr9_6322.phylip" (19 taxa, 749 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: GTRG


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	-1926.0074	3947.9039	0.5892	0.5892
GTRG	44	-1927.9005	3949.4260	0.2753	0.8644
GTRI	44	-1928.6100	3950.8450	0.1354	0.9998
HKYIG	41	-1939.2572	3965.3857	0.0001	0.9999
HKYG	40	-1941.5133	3967.6593	0.0000	1.0000
HKYI	40	-1941.6065	3967.8458	0.0000	1.0000
SYMIG	42	-1942.0039	3973.1239	0.0000	1.0000
SYMG	41	-1944.0032	3974.8776	0.0000	1.0000
SYMI	41	-1944.5454	3975.9622	0.0000	1.0000
K2PIG	38	-1956.9617	3994.0981	0.0000	1.0000
K2PI	37	-1959.5397	3997.0345	0.0000	1.0000
K2PG	37	-1959.6346	3997.2241	0.0000	1.0000
GTR	43	-1976.6483	4044.6640	0.0000	1.0000
F81IG	40	-1986.3105	4057.2537	0.0000	1.0000
F81G	39	-1988.3175	4059.0355	0.0000	1.0000
F81I	39	-1988.3713	4059.1431	0.0000	1.0000
HKY	39	-1991.8504	4066.1014	0.0000	1.0000
SYM	40	-1993.4334	4071.4996	0.0000	1.0000
JC69IG	37	-2006.6875	4091.3300	0.0000	1.0000
JC69G	36	-2008.5505	4092.8426	0.0000	1.0000
JC69I	36	-2008.6339	4093.0093	0.0000	1.0000
K2P	36	-2011.9465	4099.6346	0.0000	1.0000
F81	38	-2038.3969	4156.9684	0.0000	1.0000
JC69	35	-2057.9772	4189.4887	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1926.0074	3942.0148	0.6208	0.6208
GTRG	44	-1927.9005	3943.8010	0.2541	0.8749
GTRI	44	-1928.6100	3945.2200	0.1250	0.9999
HKYIG	41	-1939.2572	3960.5144	0.0001	1.0000
HKYG	40	-1941.5133	3963.0266	0.0000	1.0000
HKYI	40	-1941.6065	3963.2130	0.0000	1.0000
SYMIG	42	-1942.0039	3968.0078	0.0000	1.0000
SYMG	41	-1944.0032	3970.0063	0.0000	1.0000
SYMI	41	-1944.5454	3971.0909	0.0000	1.0000
K2PIG	38	-1956.9617	3989.9235	0.0000	1.0000
K2PI	37	-1959.5397	3993.0795	0.0000	1.0000
K2PG	37	-1959.6346	3993.2691	0.0000	1.0000
GTR	43	-1976.6483	4039.2966	0.0000	1.0000
F81IG	40	-1986.3105	4052.6210	0.0000	1.0000
F81G	39	-1988.3175	4054.6350	0.0000	1.0000
F81I	39	-1988.3713	4054.7425	0.0000	1.0000
HKY	39	-1991.8504	4061.7009	0.0000	1.0000
SYM	40	-1993.4334	4066.8668	0.0000	1.0000
JC69IG	37	-2006.6875	4087.3750	0.0000	1.0000
JC69G	36	-2008.5505	4089.1010	0.0000	1.0000
JC69I	36	-2008.6339	4089.2678	0.0000	1.0000
K2P	36	-2011.9465	4095.8930	0.0000	1.0000
F81	38	-2038.3969	4152.7938	0.0000	1.0000
JC69	35	-2057.9772	4185.9543	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-1927.9005	4147.0256	0.3038	0.3038
HKYG	40	-1941.5133	4147.7761	0.2087	0.5126
HKYI	40	-1941.6065	4147.9626	0.1902	0.7027
GTRI	44	-1928.6100	4148.4445	0.1494	0.8522
GTRIG	45	-1926.0074	4149.8581	0.0737	0.9259
HKYIG	41	-1939.2572	4149.8827	0.0728	0.9987
SYMG	41	-1944.0032	4159.3746	0.0006	0.9993
SYMI	41	-1944.5454	4160.4592	0.0004	0.9997
SYMIG	42	-1942.0039	4161.9948	0.0002	0.9998
K2PI	37	-1959.5397	4163.9728	0.0001	0.9999
K2PG	37	-1959.6346	4164.1625	0.0001	1.0000
K2PIG	38	-1956.9617	4165.4355	0.0000	1.0000
F81G	39	-1988.3175	4234.7658	0.0000	1.0000
F81I	39	-1988.3713	4234.8733	0.0000	1.0000
F81IG	40	-1986.3105	4237.3705	0.0000	1.0000
GTR	43	-1976.6483	4237.9024	0.0000	1.0000
HKY	39	-1991.8504	4241.8317	0.0000	1.0000
SYM	40	-1993.4334	4251.6164	0.0000	1.0000
JC69G	36	-2008.5505	4255.3756	0.0000	1.0000
JC69I	36	-2008.6339	4255.5424	0.0000	1.0000
JC69IG	37	-2006.6875	4258.2683	0.0000	1.0000
K2P	36	-2011.9465	4262.1676	0.0000	1.0000
F81	38	-2038.3969	4328.3059	0.0000	1.0000
JC69	35	-2057.9772	4347.6102	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/chr9_6322.phylip = 1 - 749;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6322.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/chr9_6322.phylip = 1 - 749;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6322.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6322.phylip = 1 - 749;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6322.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;


-------------------------------------------------------------
End of Output

