
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:23 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_1700.phylip" (19 taxa, 486 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
Minimum BIC  model: K2PG


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
HKYG	40	-1938.4476	3964.2660	0.5851	0.5851
HKYIG	41	-1938.3276	3966.4120	0.2001	0.7852
K2PG	37	-1943.9482	3968.1732	0.0829	0.8681
GTRG	44	-1935.6281	3968.2358	0.0804	0.9485
K2PIG	38	-1944.0611	3970.7531	0.0228	0.9713
HKYI	40	-1941.8541	3971.0790	0.0194	0.9907
SYMG	41	-1941.9365	3973.6297	0.0054	0.9962
K2PI	37	-1947.2138	3974.7044	0.0032	0.9993
SYMI	41	-1944.4133	3978.5834	0.0005	0.9998
GTRIG	45	-1940.5756	3980.5602	0.0002	0.9999
GTRI	44	-1943.1949	3983.3693	0.0000	1.0000
SYMIG	42	-1947.0483	3986.2501	0.0000	1.0000
HKY	39	-1985.5146	4056.0248	0.0000	1.0000
K2P	36	-1990.2970	4058.5271	0.0000	1.0000
GTR	43	-1982.6446	4059.8503	0.0000	1.0000
SYM	40	-1986.5254	4060.4216	0.0000	1.0000
JC69G	36	-2000.4078	4078.7488	0.0000	1.0000
F81G	39	-1996.9424	4078.8803	0.0000	1.0000
F81IG	40	-2000.8703	4089.1115	0.0000	1.0000
JC69IG	37	-2004.5188	4089.3144	0.0000	1.0000
F81I	39	-2002.8218	4090.6391	0.0000	1.0000
JC69I	36	-2008.2558	4094.4448	0.0000	1.0000
JC69	35	-2042.0430	4159.6861	0.0000	1.0000
F81	38	-2038.9167	4160.4643	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1938.4476	3956.8953	0.5318	0.5318
HKYIG	41	-1938.3276	3958.6552	0.2206	0.7524
GTRG	44	-1935.6281	3959.2562	0.1633	0.9157
K2PG	37	-1943.9482	3961.8964	0.0436	0.9594
HKYI	40	-1941.8541	3963.7082	0.0176	0.9770
K2PIG	38	-1944.0611	3964.1223	0.0143	0.9913
SYMG	41	-1941.9365	3965.8730	0.0060	0.9973
K2PI	37	-1947.2138	3968.4277	0.0017	0.9990
SYMI	41	-1944.4133	3970.8267	0.0005	0.9995
GTRIG	45	-1940.5756	3971.1511	0.0004	0.9999
GTRI	44	-1943.1949	3974.3897	0.0001	1.0000
SYMIG	42	-1947.0483	3978.0966	0.0000	1.0000
HKY	39	-1985.5146	4049.0293	0.0000	1.0000
GTR	43	-1982.6446	4051.2892	0.0000	1.0000
K2P	36	-1990.2970	4052.5939	0.0000	1.0000
SYM	40	-1986.5254	4053.0508	0.0000	1.0000
F81G	39	-1996.9424	4071.8847	0.0000	1.0000
JC69G	36	-2000.4078	4072.8156	0.0000	1.0000
F81IG	40	-2000.8703	4081.7407	0.0000	1.0000
JC69IG	37	-2004.5188	4083.0377	0.0000	1.0000
F81I	39	-2002.8218	4083.6436	0.0000	1.0000
JC69I	36	-2008.2558	4088.5116	0.0000	1.0000
F81	38	-2038.9167	4153.8334	0.0000	1.0000
JC69	35	-2042.0430	4154.0861	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1943.9482	4116.7861	0.9062	0.9062
K2PIG	38	-1944.0611	4123.1982	0.0367	0.9429
K2PI	37	-1947.2138	4123.3174	0.0346	0.9775
HKYG	40	-1938.4476	4124.3436	0.0207	0.9982
HKYIG	41	-1938.3276	4130.2898	0.0011	0.9993
HKYI	40	-1941.8541	4131.1565	0.0007	1.0000
SYMG	41	-1941.9365	4137.5075	0.0000	1.0000
SYMI	41	-1944.4133	4142.4612	0.0000	1.0000
GTRG	44	-1935.6281	4143.4494	0.0000	1.0000
SYMIG	42	-1947.0483	4153.9174	0.0000	1.0000
GTRI	44	-1943.1949	4158.5829	0.0000	1.0000
GTRIG	45	-1940.5756	4159.5305	0.0000	1.0000
K2P	36	-1990.2970	4203.2974	0.0000	1.0000
HKY	39	-1985.5146	4212.2914	0.0000	1.0000
SYM	40	-1986.5254	4220.4991	0.0000	1.0000
JC69G	36	-2000.4078	4223.5191	0.0000	1.0000
GTR	43	-1982.6446	4231.2962	0.0000	1.0000
F81G	39	-1996.9424	4235.1469	0.0000	1.0000
JC69IG	37	-2004.5188	4237.9274	0.0000	1.0000
JC69I	36	-2008.2558	4239.2152	0.0000	1.0000
F81I	39	-2002.8218	4246.9057	0.0000	1.0000
F81IG	40	-2000.8703	4249.1890	0.0000	1.0000
JC69	35	-2042.0430	4300.6034	0.0000	1.0000
F81	38	-2038.9167	4312.9093	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1700.phylip = 1 - 486;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1700.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1700.phylip = 1 - 486;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1700.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;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1700.phylip = 1 - 486;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1700.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

