
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:35 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_5246.phylip" (19 taxa, 816 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1944.1240	3981.3841	0.4459	0.4459
GTRI	44	-1944.5669	3982.2699	0.2864	0.7323
GTRIG	45	-1943.7323	3982.8413	0.2152	0.9475
HKYG	40	-1951.4506	3987.1335	0.0252	0.9727
HKYI	40	-1951.9318	3988.0958	0.0156	0.9882
HKYIG	41	-1951.1010	3988.6516	0.0118	1.0000
K2PG	37	-1967.7709	4013.1561	0.0000	1.0000
K2PI	37	-1968.2889	4014.1922	0.0000	1.0000
SYMG	41	-1964.0410	4014.5316	0.0000	1.0000
K2PIG	38	-1967.4178	4014.6503	0.0000	1.0000
SYMI	41	-1964.5338	4015.5173	0.0000	1.0000
SYMIG	42	-1963.6850	4016.0426	0.0000	1.0000
GTR	43	-1962.6323	4016.1661	0.0000	1.0000
HKY	39	-1968.4410	4018.9026	0.0000	1.0000
K2P	36	-1984.1909	4043.8016	0.0000	1.0000
F81G	39	-1981.4137	4044.8480	0.0000	1.0000
F81I	39	-1981.8500	4045.7207	0.0000	1.0000
SYM	40	-1980.9247	4046.0817	0.0000	1.0000
F81IG	40	-1981.1529	4046.5381	0.0000	1.0000
JC69G	36	-1995.4159	4066.2516	0.0000	1.0000
JC69I	36	-1995.8704	4067.1606	0.0000	1.0000
JC69IG	37	-1995.1460	4067.9065	0.0000	1.0000
F81	38	-1997.3676	4074.5499	0.0000	1.0000
JC69	35	-2011.2049	4095.6406	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1944.1240	3976.2480	0.4418	0.4418
GTRI	44	-1944.5669	3977.1337	0.2837	0.7256
GTRIG	45	-1943.7323	3977.4647	0.2405	0.9660
HKYG	40	-1951.4506	3982.9013	0.0159	0.9819
HKYI	40	-1951.9318	3983.8635	0.0098	0.9917
HKYIG	41	-1951.1010	3984.2019	0.0083	1.0000
K2PG	37	-1967.7709	4009.5417	0.0000	1.0000
SYMG	41	-1964.0410	4010.0820	0.0000	1.0000
K2PI	37	-1968.2889	4010.5778	0.0000	1.0000
K2PIG	38	-1967.4178	4010.8356	0.0000	1.0000
SYMI	41	-1964.5338	4011.0677	0.0000	1.0000
GTR	43	-1962.6323	4011.2645	0.0000	1.0000
SYMIG	42	-1963.6850	4011.3699	0.0000	1.0000
HKY	39	-1968.4410	4014.8820	0.0000	1.0000
K2P	36	-1984.1909	4040.3819	0.0000	1.0000
F81G	39	-1981.4137	4040.8274	0.0000	1.0000
F81I	39	-1981.8500	4041.7001	0.0000	1.0000
SYM	40	-1980.9247	4041.8495	0.0000	1.0000
F81IG	40	-1981.1529	4042.3059	0.0000	1.0000
JC69G	36	-1995.4159	4062.8319	0.0000	1.0000
JC69I	36	-1995.8704	4063.7409	0.0000	1.0000
JC69IG	37	-1995.1460	4064.2921	0.0000	1.0000
F81	38	-1997.3676	4070.7352	0.0000	1.0000
JC69	35	-2011.2049	4092.4099	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1951.4506	4171.0779	0.5971	0.5971
HKYI	40	-1951.9318	4172.0401	0.3691	0.9662
HKYIG	41	-1951.1010	4177.0829	0.0297	0.9958
GTRG	44	-1944.1240	4183.2422	0.0014	0.9972
K2PG	37	-1967.7709	4183.6050	0.0011	0.9983
GTRI	44	-1944.5669	4184.1280	0.0009	0.9992
K2PI	37	-1968.2889	4184.6411	0.0007	0.9999
GTRIG	45	-1943.7323	4189.1633	0.0001	0.9999
K2PIG	38	-1967.4178	4189.6033	0.0001	1.0000
HKY	39	-1968.4410	4198.3541	0.0000	1.0000
SYMG	41	-1964.0410	4202.9630	0.0000	1.0000
SYMI	41	-1964.5338	4203.9487	0.0000	1.0000
SYMIG	42	-1963.6850	4208.9553	0.0000	1.0000
K2P	36	-1984.1909	4209.7408	0.0000	1.0000
GTR	43	-1962.6323	4213.5543	0.0000	1.0000
F81G	39	-1981.4137	4224.2996	0.0000	1.0000
F81I	39	-1981.8500	4225.1722	0.0000	1.0000
SYM	40	-1980.9247	4230.0260	0.0000	1.0000
F81IG	40	-1981.1529	4230.4825	0.0000	1.0000
JC69G	36	-1995.4159	4232.1908	0.0000	1.0000
JC69I	36	-1995.8704	4233.0998	0.0000	1.0000
JC69IG	37	-1995.1460	4238.3554	0.0000	1.0000
F81	38	-1997.3676	4249.5030	0.0000	1.0000
JC69	35	-2011.2049	4257.0644	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/chr9_5246.phylip = 1 - 816;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5246.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/chr9_5246.phylip = 1 - 816;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5246.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5246.phylip = 1 - 816;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5246.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

