
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:31 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/chr4_6739.phylip" (19 taxa, 584 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	-3423.6136	6942.5741	0.6515	0.6515
GTRIG	45	-3423.5162	6944.7275	0.2220	0.8735
HKYG	40	-3430.8172	6947.6749	0.0508	0.9243
SYMG	41	-3429.8161	6947.9864	0.0435	0.9678
HKYIG	41	-3430.7129	6949.7800	0.0177	0.9856
SYMIG	42	-3429.7590	6950.1945	0.0144	1.0000
K2PG	37	-3444.6795	6968.5092	0.0000	1.0000
K2PIG	38	-3444.5347	6970.5080	0.0000	1.0000
GTRI	44	-3441.3747	6978.0964	0.0000	1.0000
HKYI	40	-3448.3609	6982.7623	0.0000	1.0000
SYMI	41	-3448.5572	6985.4686	0.0000	1.0000
K2PI	37	-3461.2426	7001.6355	0.0000	1.0000
GTR	43	-3497.4890	7087.9853	0.0000	1.0000
SYM	40	-3502.1671	7090.3747	0.0000	1.0000
HKY	39	-3507.9222	7099.5796	0.0000	1.0000
F81IG	40	-3511.0173	7108.0752	0.0000	1.0000
F81G	39	-3512.7369	7109.2092	0.0000	1.0000
K2P	36	-3520.4902	7117.8507	0.0000	1.0000
F81I	39	-3525.7288	7135.1928	0.0000	1.0000
JC69G	36	-3531.0169	7138.9040	0.0000	1.0000
JC69IG	37	-3530.9405	7141.0311	0.0000	1.0000
JC69I	36	-3545.8353	7168.5407	0.0000	1.0000
F81	38	-3585.4237	7252.2859	0.0000	1.0000
JC69	35	-3601.1715	7276.9415	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3423.6136	6935.2271	0.6582	0.6582
GTRIG	45	-3423.5162	6937.0323	0.2669	0.9252
SYMG	41	-3429.8161	6941.6322	0.0268	0.9519
HKYG	40	-3430.8172	6941.6344	0.0267	0.9787
HKYIG	41	-3430.7129	6943.4258	0.0109	0.9896
SYMIG	42	-3429.7590	6943.5180	0.0104	1.0000
K2PG	37	-3444.6795	6963.3590	0.0000	1.0000
K2PIG	38	-3444.5347	6965.0695	0.0000	1.0000
GTRI	44	-3441.3747	6970.7495	0.0000	1.0000
HKYI	40	-3448.3609	6976.7218	0.0000	1.0000
SYMI	41	-3448.5572	6979.1144	0.0000	1.0000
K2PI	37	-3461.2426	6996.4853	0.0000	1.0000
GTR	43	-3497.4890	7080.9779	0.0000	1.0000
SYM	40	-3502.1671	7084.3341	0.0000	1.0000
HKY	39	-3507.9222	7093.8443	0.0000	1.0000
F81IG	40	-3511.0173	7102.0346	0.0000	1.0000
F81G	39	-3512.7369	7103.4739	0.0000	1.0000
K2P	36	-3520.4902	7112.9805	0.0000	1.0000
F81I	39	-3525.7288	7129.4575	0.0000	1.0000
JC69G	36	-3531.0169	7134.0338	0.0000	1.0000
JC69IG	37	-3530.9405	7135.8809	0.0000	1.0000
JC69I	36	-3545.8353	7163.6705	0.0000	1.0000
F81	38	-3585.4237	7246.8474	0.0000	1.0000
JC69	35	-3601.1715	7272.3430	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3430.8172	7116.4305	0.8462	0.8462
SYMG	41	-3429.8161	7120.7981	0.0953	0.9415
HKYIG	41	-3430.7129	7122.5917	0.0389	0.9804
K2PG	37	-3444.6795	7125.0454	0.0114	0.9918
SYMIG	42	-3429.7590	7127.0539	0.0042	0.9960
GTRG	44	-3423.6136	7127.5028	0.0033	0.9993
K2PIG	38	-3444.5347	7131.1257	0.0005	0.9998
GTRIG	45	-3423.5162	7133.6779	0.0002	1.0000
HKYI	40	-3448.3609	7151.5178	0.0000	1.0000
K2PI	37	-3461.2426	7158.1716	0.0000	1.0000
SYMI	41	-3448.5572	7158.2803	0.0000	1.0000
GTRI	44	-3441.3747	7163.0251	0.0000	1.0000
SYM	40	-3502.1671	7259.1302	0.0000	1.0000
HKY	39	-3507.9222	7264.2705	0.0000	1.0000
GTR	43	-3497.4890	7268.8837	0.0000	1.0000
K2P	36	-3520.4902	7270.2969	0.0000	1.0000
F81G	39	-3512.7369	7273.9000	0.0000	1.0000
F81IG	40	-3511.0173	7276.8307	0.0000	1.0000
JC69G	36	-3531.0169	7291.3502	0.0000	1.0000
JC69IG	37	-3530.9405	7297.5673	0.0000	1.0000
F81I	39	-3525.7288	7299.8836	0.0000	1.0000
JC69I	36	-3545.8353	7320.9869	0.0000	1.0000
F81	38	-3585.4237	7412.9036	0.0000	1.0000
JC69	35	-3601.1715	7425.2895	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/chr4_6739.phylip = 1 - 584;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_6739.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/chr4_6739.phylip = 1 - 584;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_6739.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/chr4_6739.phylip = 1 - 584;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_6739.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

