
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:09 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/chr3_451.phylip" (19 taxa, 650 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	-1964.4419	4023.4292	0.4383	0.4383
HKYG	40	-1969.7068	4024.7995	0.2209	0.6592
GTRIG	45	-1964.2155	4025.2853	0.1733	0.8324
HKYIG	41	-1969.5059	4026.6762	0.0864	0.9189
GTRI	44	-1966.5560	4027.6574	0.0529	0.9718
HKYI	40	-1971.7645	4028.9149	0.0282	1.0000
SYMG	41	-1980.5019	4048.6683	0.0000	1.0000
SYMIG	42	-1980.3010	4050.5525	0.0000	1.0000
SYMI	41	-1982.6666	4052.9978	0.0000	1.0000
K2PG	37	-1987.8796	4054.3539	0.0000	1.0000
K2PIG	38	-1987.7047	4056.2604	0.0000	1.0000
K2PI	37	-1989.9365	4058.4678	0.0000	1.0000
F81G	39	-1995.0721	4073.2590	0.0000	1.0000
F81IG	40	-1994.8230	4075.0318	0.0000	1.0000
F81I	39	-1997.3487	4077.8122	0.0000	1.0000
HKY	39	-1998.5039	4080.1226	0.0000	1.0000
GTR	43	-1994.4094	4081.0631	0.0000	1.0000
JC69G	36	-2013.0458	4102.4375	0.0000	1.0000
SYM	40	-2008.7548	4102.8955	0.0000	1.0000
JC69IG	37	-2012.8472	4104.2891	0.0000	1.0000
K2P	36	-2015.0882	4106.5223	0.0000	1.0000
JC69I	36	-2015.1880	4106.7218	0.0000	1.0000
F81	38	-2022.9094	4126.6699	0.0000	1.0000
JC69	35	-2039.8700	4153.8443	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1964.4419	4016.8837	0.4933	0.4933
GTRIG	45	-1964.2155	4018.4310	0.2276	0.7208
HKYG	40	-1969.7068	4019.4136	0.1392	0.8600
HKYIG	41	-1969.5059	4021.0117	0.0626	0.9227
GTRI	44	-1966.5560	4021.1119	0.0596	0.9822
HKYI	40	-1971.7645	4023.5290	0.0178	1.0000
SYMG	41	-1980.5019	4043.0038	0.0000	1.0000
SYMIG	42	-1980.3010	4044.6019	0.0000	1.0000
SYMI	41	-1982.6666	4047.3333	0.0000	1.0000
K2PG	37	-1987.8796	4049.7591	0.0000	1.0000
K2PIG	38	-1987.7047	4051.4094	0.0000	1.0000
K2PI	37	-1989.9365	4053.8730	0.0000	1.0000
F81G	39	-1995.0721	4068.1443	0.0000	1.0000
F81IG	40	-1994.8230	4069.6459	0.0000	1.0000
F81I	39	-1997.3487	4072.6974	0.0000	1.0000
GTR	43	-1994.4094	4074.8189	0.0000	1.0000
HKY	39	-1998.5039	4075.0078	0.0000	1.0000
SYM	40	-2008.7548	4097.5097	0.0000	1.0000
JC69G	36	-2013.0458	4098.0916	0.0000	1.0000
JC69IG	37	-2012.8472	4099.6944	0.0000	1.0000
K2P	36	-2015.0882	4102.1764	0.0000	1.0000
JC69I	36	-2015.1880	4102.3759	0.0000	1.0000
F81	38	-2022.9094	4121.8188	0.0000	1.0000
JC69	35	-2039.8700	4149.7401	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1969.7068	4198.4925	0.8500	0.8500
HKYI	40	-1971.7645	4202.6079	0.1086	0.9586
HKYIG	41	-1969.5059	4204.5676	0.0408	0.9993
GTRG	44	-1964.4419	4213.8705	0.0004	0.9997
K2PG	37	-1987.8796	4215.4071	0.0002	0.9999
GTRI	44	-1966.5560	4218.0987	0.0000	0.9999
K2PI	37	-1989.9365	4219.5210	0.0000	1.0000
GTRIG	45	-1964.2155	4219.8948	0.0000	1.0000
K2PIG	38	-1987.7047	4221.5343	0.0000	1.0000
SYMG	41	-1980.5019	4226.5597	0.0000	1.0000
SYMI	41	-1982.6666	4230.8892	0.0000	1.0000
SYMIG	42	-1980.3010	4232.6348	0.0000	1.0000
F81G	39	-1995.0721	4242.7462	0.0000	1.0000
F81I	39	-1997.3487	4247.2994	0.0000	1.0000
F81IG	40	-1994.8230	4248.7248	0.0000	1.0000
HKY	39	-1998.5039	4249.6098	0.0000	1.0000
JC69G	36	-2013.0458	4259.2626	0.0000	1.0000
K2P	36	-2015.0882	4263.3474	0.0000	1.0000
JC69I	36	-2015.1880	4263.5469	0.0000	1.0000
JC69IG	37	-2012.8472	4265.3423	0.0000	1.0000
GTR	43	-1994.4094	4267.3287	0.0000	1.0000
SYM	40	-2008.7548	4276.5886	0.0000	1.0000
F81	38	-2022.9094	4291.9437	0.0000	1.0000
JC69	35	-2039.8700	4306.4341	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/chr3_451.phylip = 1 - 650;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_451.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/chr3_451.phylip = 1 - 650;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_451.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/chr3_451.phylip = 1 - 650;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_451.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

