
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:53 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/chr2_12858.phylip" (19 taxa, 377 characters)

Minimum AIC  model: GTRG
Minimum AICc model: SYMG
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
SYMG	41	-2000.3967	4093.0739	0.3796	0.3796
GTRG	44	-1996.7314	4093.3905	0.3241	0.7037
SYMIG	42	-2000.3954	4095.6051	0.1071	0.8108
GTRIG	45	-1996.7312	4095.9700	0.0892	0.9000
K2PG	37	-2007.1492	4096.5934	0.0653	0.9653
K2PIG	38	-2007.1431	4099.0554	0.0191	0.9844
HKYG	40	-2005.3766	4100.5151	0.0092	0.9936
HKYIG	41	-2005.3655	4103.0116	0.0026	0.9962
GTRI	44	-2001.6645	4103.2567	0.0023	0.9986
SYMI	41	-2006.2036	4104.6877	0.0011	0.9997
K2PI	37	-2012.7503	4107.7956	0.0002	1.0000
HKYI	40	-2010.9893	4111.7405	0.0000	1.0000
JC69G	36	-2039.6049	4159.0452	0.0000	1.0000
JC69IG	37	-2039.6053	4161.5055	0.0000	1.0000
F81G	39	-2037.3892	4162.0365	0.0000	1.0000
F81IG	40	-2037.3896	4164.5412	0.0000	1.0000
JC69I	36	-2044.7609	4169.3572	0.0000	1.0000
F81I	39	-2042.4450	4172.1482	0.0000	1.0000
SYM	40	-2053.4967	4196.7553	0.0000	1.0000
K2P	36	-2061.0310	4201.8973	0.0000	1.0000
GTR	43	-2052.3612	4202.0858	0.0000	1.0000
HKY	39	-2059.4983	4206.2548	0.0000	1.0000
JC69	35	-2092.1659	4261.7217	0.0000	1.0000
F81	38	-2090.7796	4266.3285	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1996.7314	4081.4627	0.4676	0.4676
SYMG	41	-2000.3967	4082.7933	0.2404	0.7080
GTRIG	45	-1996.7312	4083.4625	0.1721	0.8801
SYMIG	42	-2000.3954	4084.7907	0.0886	0.9687
K2PG	37	-2007.1492	4088.2984	0.0153	0.9840
K2PIG	38	-2007.1431	4090.2862	0.0057	0.9897
HKYG	40	-2005.3766	4090.7532	0.0045	0.9942
GTRI	44	-2001.6645	4091.3290	0.0034	0.9975
HKYIG	41	-2005.3655	4092.7310	0.0017	0.9992
SYMI	41	-2006.2036	4094.4071	0.0007	0.9999
K2PI	37	-2012.7503	4099.5007	0.0001	1.0000
HKYI	40	-2010.9893	4101.9786	0.0000	1.0000
JC69G	36	-2039.6049	4151.2099	0.0000	1.0000
F81G	39	-2037.3892	4152.7784	0.0000	1.0000
JC69IG	37	-2039.6053	4153.2105	0.0000	1.0000
F81IG	40	-2037.3896	4154.7793	0.0000	1.0000
JC69I	36	-2044.7609	4161.5219	0.0000	1.0000
F81I	39	-2042.4450	4162.8900	0.0000	1.0000
SYM	40	-2053.4967	4186.9934	0.0000	1.0000
GTR	43	-2052.3612	4190.7225	0.0000	1.0000
K2P	36	-2061.0310	4194.0620	0.0000	1.0000
HKY	39	-2059.4983	4196.9967	0.0000	1.0000
JC69	35	-2092.1659	4254.3317	0.0000	1.0000
F81	38	-2090.7796	4257.5592	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2007.1492	4233.7915	0.9410	0.9410
K2PIG	38	-2007.1431	4239.7115	0.0488	0.9897
SYMG	41	-2000.3967	4244.0154	0.0057	0.9954
K2PI	37	-2012.7503	4244.9937	0.0035	0.9989
HKYG	40	-2005.3766	4248.0430	0.0008	0.9996
SYMIG	42	-2000.3954	4249.9450	0.0003	0.9999
HKYIG	41	-2005.3655	4253.9531	0.0000	0.9999
GTRG	44	-1996.7314	4254.4815	0.0000	1.0000
SYMI	41	-2006.2036	4255.6292	0.0000	1.0000
HKYI	40	-2010.9893	4259.2684	0.0000	1.0000
GTRIG	45	-1996.7312	4260.4135	0.0000	1.0000
GTRI	44	-2001.6645	4264.3478	0.0000	1.0000
JC69G	36	-2039.6049	4292.7707	0.0000	1.0000
JC69IG	37	-2039.6053	4298.7036	0.0000	1.0000
JC69I	36	-2044.7609	4303.0827	0.0000	1.0000
F81G	39	-2037.3892	4306.1359	0.0000	1.0000
F81IG	40	-2037.3896	4312.0691	0.0000	1.0000
F81I	39	-2042.4450	4316.2476	0.0000	1.0000
K2P	36	-2061.0310	4335.6228	0.0000	1.0000
SYM	40	-2053.4967	4344.2832	0.0000	1.0000
HKY	39	-2059.4983	4350.3542	0.0000	1.0000
GTR	43	-2052.3612	4359.8090	0.0000	1.0000
JC69	35	-2092.1659	4391.9603	0.0000	1.0000
F81	38	-2090.7796	4406.9846	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/chr2_12858.phylip = 1 - 377;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12858.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 (SYMG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12858.phylip = 1 - 377;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12858.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=Fixed(Equal);
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/chr2_12858.phylip = 1 - 377;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12858.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

