
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:37 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_3223.phylip" (19 taxa, 730 characters)

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


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	-1922.8187	3941.6901	0.9355	0.9355
GTRG	44	-1926.7381	3947.2572	0.0578	0.9933
GTRI	44	-1928.8985	3951.5779	0.0067	1.0000
HKYG	40	-1939.6074	3963.9754	0.0000	1.0000
HKYIG	41	-1939.1686	3965.3430	0.0000	1.0000
HKYI	40	-1940.7907	3966.3419	0.0000	1.0000
GTR	43	-1949.2027	3989.9214	0.0000	1.0000
HKY	39	-1961.0191	4004.5599	0.0000	1.0000
SYMG	41	-1962.3062	4011.6183	0.0000	1.0000
SYMIG	42	-1961.6152	4012.4881	0.0000	1.0000
SYMI	41	-1963.8596	4014.7250	0.0000	1.0000
K2PG	37	-1968.8216	4015.7067	0.0000	1.0000
K2PIG	38	-1968.3037	4016.8969	0.0000	1.0000
K2PI	37	-1969.9336	4017.9307	0.0000	1.0000
SYM	40	-1984.7680	4054.2965	0.0000	1.0000
K2P	36	-1991.4031	4058.6504	0.0000	1.0000
F81G	39	-1994.4665	4071.4547	0.0000	1.0000
F81IG	40	-1994.0250	4072.8106	0.0000	1.0000
F81I	39	-1995.6831	4073.8879	0.0000	1.0000
F81	38	-2014.4377	4109.1647	0.0000	1.0000
JC69G	36	-2018.6455	4113.1352	0.0000	1.0000
JC69IG	37	-2018.1423	4114.3481	0.0000	1.0000
JC69I	36	-2019.9104	4115.6649	0.0000	1.0000
JC69	35	-2039.3194	4152.2699	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1922.8187	3935.6374	0.9432	0.9432
GTRG	44	-1926.7381	3941.4762	0.0509	0.9941
GTRI	44	-1928.8985	3945.7969	0.0059	1.0000
HKYG	40	-1939.6074	3959.2148	0.0000	1.0000
HKYIG	41	-1939.1686	3960.3372	0.0000	1.0000
HKYI	40	-1940.7907	3961.5813	0.0000	1.0000
GTR	43	-1949.2027	3984.4054	0.0000	1.0000
HKY	39	-1961.0191	4000.0381	0.0000	1.0000
SYMG	41	-1962.3062	4006.6125	0.0000	1.0000
SYMIG	42	-1961.6152	4007.2305	0.0000	1.0000
SYMI	41	-1963.8596	4009.7191	0.0000	1.0000
K2PG	37	-1968.8216	4011.6431	0.0000	1.0000
K2PIG	38	-1968.3037	4012.6074	0.0000	1.0000
K2PI	37	-1969.9336	4013.8672	0.0000	1.0000
SYM	40	-1984.7680	4049.5359	0.0000	1.0000
K2P	36	-1991.4031	4054.8062	0.0000	1.0000
F81G	39	-1994.4665	4066.9330	0.0000	1.0000
F81IG	40	-1994.0250	4068.0501	0.0000	1.0000
F81I	39	-1995.6831	4069.3662	0.0000	1.0000
F81	38	-2014.4377	4104.8753	0.0000	1.0000
JC69G	36	-2018.6455	4109.2910	0.0000	1.0000
JC69IG	37	-2018.1423	4110.2846	0.0000	1.0000
JC69I	36	-2019.9104	4111.8207	0.0000	1.0000
JC69	35	-2039.3194	4148.6388	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRIG	45	-1922.8187	4142.3244	0.3843	0.3843
HKYG	40	-1939.6074	4142.9366	0.2829	0.6672
GTRG	44	-1926.7381	4143.5702	0.2061	0.8733
HKYI	40	-1940.7907	4145.3031	0.0867	0.9600
GTRI	44	-1928.8985	4147.8909	0.0238	0.9838
HKYIG	41	-1939.1686	4148.6520	0.0162	1.0000
HKY	39	-1961.0191	4179.1669	0.0000	1.0000
K2PG	37	-1968.8216	4181.5858	0.0000	1.0000
GTR	43	-1949.2027	4181.9063	0.0000	1.0000
K2PI	37	-1969.9336	4183.8098	0.0000	1.0000
K2PIG	38	-1968.3037	4187.1431	0.0000	1.0000
SYMG	41	-1962.3062	4194.9273	0.0000	1.0000
SYMI	41	-1963.8596	4198.0340	0.0000	1.0000
SYMIG	42	-1961.6152	4200.1384	0.0000	1.0000
K2P	36	-1991.4031	4220.1558	0.0000	1.0000
SYM	40	-1984.7680	4233.2577	0.0000	1.0000
F81G	39	-1994.4665	4246.0617	0.0000	1.0000
F81I	39	-1995.6831	4248.4949	0.0000	1.0000
F81IG	40	-1994.0250	4251.7719	0.0000	1.0000
JC69G	36	-2018.6455	4274.6406	0.0000	1.0000
JC69I	36	-2019.9104	4277.1703	0.0000	1.0000
F81	38	-2014.4377	4279.4110	0.0000	1.0000
JC69IG	37	-2018.1423	4280.2272	0.0000	1.0000
JC69	35	-2039.3194	4309.3954	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_3223.phylip = 1 - 730;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3223.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_3223.phylip = 1 - 730;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3223.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 (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3223.phylip = 1 - 730;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3223.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;


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End of Output

