
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:35 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/chr3_9709.phylip" (19 taxa, 626 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-1981.1520	4047.9109	0.3768	0.3768
HKYI	40	-1981.4428	4048.4925	0.2817	0.6586
HKYIG	41	-1980.7424	4049.3821	0.1806	0.8392
GTRG	44	-1978.0579	4050.9316	0.0832	0.9224
GTRI	44	-1978.7882	4052.3922	0.0401	0.9625
GTRIG	45	-1977.6929	4052.5238	0.0375	1.0000
K2PG	37	-1998.7963	4076.3749	0.0000	1.0000
K2PI	37	-1999.0579	4076.8982	0.0000	1.0000
K2PIG	38	-1998.4515	4077.9523	0.0000	1.0000
SYMG	41	-1996.1707	4080.2387	0.0000	1.0000
SYMIG	42	-1995.8186	4081.8327	0.0000	1.0000
SYMI	41	-1997.2735	4082.4442	0.0000	1.0000
F81G	39	-2014.1983	4111.7208	0.0000	1.0000
HKY	39	-2014.2996	4111.9235	0.0000	1.0000
F81IG	40	-2013.8920	4113.3909	0.0000	1.0000
F81I	39	-2015.0654	4113.4551	0.0000	1.0000
GTR	43	-2011.0814	4114.6645	0.0000	1.0000
JC69G	36	-2029.4424	4135.4077	0.0000	1.0000
JC69IG	37	-2029.1551	4137.0925	0.0000	1.0000
K2P	36	-2030.3628	4137.2485	0.0000	1.0000
JC69I	36	-2030.4085	4137.3399	0.0000	1.0000
SYM	40	-2027.3916	4140.3901	0.0000	1.0000
F81	38	-2045.2200	4171.4895	0.0000	1.0000
JC69	35	-2059.9832	4194.2377	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1981.1520	4042.3040	0.3210	0.3210
HKYI	40	-1981.4428	4042.8857	0.2400	0.5611
HKYIG	41	-1980.7424	4043.4848	0.1779	0.7390
GTRG	44	-1978.0579	4044.1157	0.1298	0.8687
GTRIG	45	-1977.6929	4045.3858	0.0688	0.9375
GTRI	44	-1978.7882	4045.5764	0.0625	1.0000
K2PG	37	-1998.7963	4071.5926	0.0000	1.0000
K2PI	37	-1999.0579	4072.1159	0.0000	1.0000
K2PIG	38	-1998.4515	4072.9029	0.0000	1.0000
SYMG	41	-1996.1707	4074.3415	0.0000	1.0000
SYMIG	42	-1995.8186	4075.6372	0.0000	1.0000
SYMI	41	-1997.2735	4076.5470	0.0000	1.0000
F81G	39	-2014.1983	4106.3966	0.0000	1.0000
HKY	39	-2014.2996	4106.5993	0.0000	1.0000
F81IG	40	-2013.8920	4107.7840	0.0000	1.0000
F81I	39	-2015.0654	4108.1308	0.0000	1.0000
GTR	43	-2011.0814	4108.1628	0.0000	1.0000
JC69G	36	-2029.4424	4130.8848	0.0000	1.0000
JC69IG	37	-2029.1551	4132.3101	0.0000	1.0000
K2P	36	-2030.3628	4132.7256	0.0000	1.0000
JC69I	36	-2030.4085	4132.8170	0.0000	1.0000
SYM	40	-2027.3916	4134.7833	0.0000	1.0000
F81	38	-2045.2200	4166.4401	0.0000	1.0000
JC69	35	-2059.9832	4189.9665	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1981.1520	4219.8781	0.5529	0.5529
HKYI	40	-1981.4428	4220.4597	0.4134	0.9663
HKYIG	41	-1980.7424	4225.4982	0.0333	0.9996
K2PG	37	-1998.7963	4235.8485	0.0002	0.9998
K2PI	37	-1999.0579	4236.3718	0.0001	0.9999
GTRG	44	-1978.0579	4239.4471	0.0000	1.0000
GTRI	44	-1978.7882	4240.9078	0.0000	1.0000
K2PIG	38	-1998.4515	4241.5982	0.0000	1.0000
GTRIG	45	-1977.6929	4245.1566	0.0000	1.0000
SYMG	41	-1996.1707	4256.3548	0.0000	1.0000
SYMI	41	-1997.2735	4258.5603	0.0000	1.0000
SYMIG	42	-1995.8186	4262.0899	0.0000	1.0000
F81G	39	-2014.1983	4279.5312	0.0000	1.0000
HKY	39	-2014.2996	4279.7340	0.0000	1.0000
F81I	39	-2015.0654	4281.2655	0.0000	1.0000
F81IG	40	-2013.8920	4285.3580	0.0000	1.0000
JC69G	36	-2029.4424	4290.7014	0.0000	1.0000
K2P	36	-2030.3628	4292.5422	0.0000	1.0000
JC69I	36	-2030.4085	4292.6336	0.0000	1.0000
JC69IG	37	-2029.1551	4296.5661	0.0000	1.0000
GTR	43	-2011.0814	4299.0548	0.0000	1.0000
SYM	40	-2027.3916	4312.3573	0.0000	1.0000
F81	38	-2045.2200	4335.1354	0.0000	1.0000
JC69	35	-2059.9832	4345.3437	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/chr3_9709.phylip = 1 - 626;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9709.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/chr3_9709.phylip = 1 - 626;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9709.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9709.phylip = 1 - 626;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9709.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

