
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:33 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/chr11_3250.phylip" (19 taxa, 526 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	-1911.1067	3920.8384	0.7913	0.7913
GTRG	44	-1913.6508	3923.5345	0.2055	0.9969
GTRI	44	-1917.9065	3932.0459	0.0029	0.9998
HKYIG	41	-1924.3715	3937.8588	0.0002	1.0000
HKYG	40	-1927.3081	3941.3790	0.0000	1.0000
SYMIG	42	-1928.9661	3949.4105	0.0000	1.0000
K2PIG	38	-1933.7954	3949.6771	0.0000	1.0000
SYMG	41	-1931.5858	3952.2874	0.0000	1.0000
K2PG	37	-1936.4993	3952.7609	0.0000	1.0000
HKYI	40	-1934.3803	3955.5235	0.0000	1.0000
K2PI	37	-1943.8946	3967.5515	0.0000	1.0000
SYMI	41	-1939.4941	3968.1040	0.0000	1.0000
F81IG	40	-1979.5135	4045.7899	0.0000	1.0000
F81G	39	-1981.9513	4048.3223	0.0000	1.0000
JC69IG	37	-1987.7527	4055.2677	0.0000	1.0000
JC69G	36	-1990.8210	4059.0899	0.0000	1.0000
F81I	39	-1989.6584	4063.7366	0.0000	1.0000
JC69I	36	-1997.4992	4072.4462	0.0000	1.0000
GTR	43	-1996.8996	4087.6498	0.0000	1.0000
HKY	39	-2011.8146	4108.0490	0.0000	1.0000
SYM	40	-2013.8023	4114.3675	0.0000	1.0000
K2P	36	-2020.8040	4119.0558	0.0000	1.0000
F81	38	-2063.0226	4208.1315	0.0000	1.0000
JC69	35	-2072.4321	4220.0071	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1911.1067	3912.2134	0.8219	0.8219
GTRG	44	-1913.6508	3915.3016	0.1755	0.9974
GTRI	44	-1917.9065	3923.8130	0.0025	0.9999
HKYIG	41	-1924.3715	3930.7431	0.0001	1.0000
HKYG	40	-1927.3081	3934.6161	0.0000	1.0000
SYMIG	42	-1928.9661	3941.9323	0.0000	1.0000
K2PIG	38	-1933.7954	3943.5909	0.0000	1.0000
SYMG	41	-1931.5858	3945.1717	0.0000	1.0000
K2PG	37	-1936.4993	3946.9986	0.0000	1.0000
HKYI	40	-1934.3803	3948.7606	0.0000	1.0000
SYMI	41	-1939.4941	3960.9883	0.0000	1.0000
K2PI	37	-1943.8946	3961.7892	0.0000	1.0000
F81IG	40	-1979.5135	4039.0270	0.0000	1.0000
F81G	39	-1981.9513	4041.9025	0.0000	1.0000
JC69IG	37	-1987.7527	4049.5054	0.0000	1.0000
JC69G	36	-1990.8210	4053.6420	0.0000	1.0000
F81I	39	-1989.6584	4057.3168	0.0000	1.0000
JC69I	36	-1997.4992	4066.9983	0.0000	1.0000
GTR	43	-1996.8996	4079.7991	0.0000	1.0000
HKY	39	-2011.8146	4101.6292	0.0000	1.0000
SYM	40	-2013.8023	4107.6047	0.0000	1.0000
K2P	36	-2020.8040	4113.6080	0.0000	1.0000
F81	38	-2063.0226	4202.0453	0.0000	1.0000
JC69	35	-2072.4321	4214.8643	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-1913.6508	4102.9749	0.3548	0.3548
GTRIG	45	-1911.1067	4104.1519	0.1969	0.5517
K2PG	37	-1936.4993	4104.8148	0.1414	0.6931
HKYG	40	-1927.3081	4105.2281	0.1150	0.8081
HKYIG	41	-1924.3715	4105.6204	0.0945	0.9026
K2PIG	38	-1933.7954	4105.6723	0.0921	0.9947
GTRI	44	-1917.9065	4111.4863	0.0050	0.9997
HKYI	40	-1934.3803	4119.3726	0.0001	0.9998
K2PI	37	-1943.8946	4119.6053	0.0001	0.9999
SYMG	41	-1931.5858	4120.0490	0.0001	1.0000
SYMIG	42	-1928.9661	4121.0749	0.0000	1.0000
SYMI	41	-1939.4941	4135.8656	0.0000	1.0000
JC69G	36	-1990.8210	4207.1929	0.0000	1.0000
JC69IG	37	-1987.7527	4207.3215	0.0000	1.0000
F81G	39	-1981.9513	4208.2493	0.0000	1.0000
F81IG	40	-1979.5135	4209.6390	0.0000	1.0000
JC69I	36	-1997.4992	4220.5492	0.0000	1.0000
F81I	39	-1989.6584	4223.6636	0.0000	1.0000
GTR	43	-1996.8996	4263.2071	0.0000	1.0000
K2P	36	-2020.8040	4267.1588	0.0000	1.0000
HKY	39	-2011.8146	4267.9760	0.0000	1.0000
SYM	40	-2013.8023	4278.2167	0.0000	1.0000
F81	38	-2063.0226	4364.1267	0.0000	1.0000
JC69	35	-2072.4321	4364.1498	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/chr11_3250.phylip = 1 - 526;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3250.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/chr11_3250.phylip = 1 - 526;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3250.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/chr11_3250.phylip = 1 - 526;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3250.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;


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End of Output

