
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:14 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/chrZ_4723.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	-2133.0448	4360.6350	0.5433	0.5433
GTRI	44	-2134.1306	4362.8066	0.1834	0.7267
GTRIG	45	-2133.0408	4362.9358	0.1719	0.8986
HKYG	40	-2139.9592	4365.3043	0.0526	0.9512
HKYI	40	-2140.4567	4366.2993	0.0320	0.9832
HKYIG	41	-2139.9629	4367.5903	0.0168	1.0000
GTR	43	-2155.6753	4403.5949	0.0000	1.0000
HKY	39	-2163.8397	4410.7942	0.0000	1.0000
K2PG	37	-2166.9658	4412.5264	0.0000	1.0000
K2PI	37	-2167.1616	4412.9179	0.0000	1.0000
K2PIG	38	-2166.9657	4414.7824	0.0000	1.0000
SYMG	41	-2164.8578	4417.3800	0.0000	1.0000
SYMI	41	-2165.0438	4417.7520	0.0000	1.0000
SYMIG	42	-2164.8577	4419.6659	0.0000	1.0000
F81G	39	-2175.3501	4433.8149	0.0000	1.0000
F81I	39	-2175.7587	4434.6321	0.0000	1.0000
F81IG	40	-2175.3522	4436.0903	0.0000	1.0000
K2P	36	-2193.9553	4464.2564	0.0000	1.0000
SYM	40	-2190.8691	4467.1241	0.0000	1.0000
JC69G	36	-2199.5926	4475.5310	0.0000	1.0000
JC69I	36	-2199.8079	4475.9617	0.0000	1.0000
JC69IG	37	-2199.5990	4477.7928	0.0000	1.0000
F81	38	-2200.1279	4481.1068	0.0000	1.0000
JC69	35	-2226.0125	4526.1291	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2133.0448	4354.0895	0.5512	0.5512
GTRIG	45	-2133.0408	4356.0815	0.2036	0.7548
GTRI	44	-2134.1306	4356.2611	0.1861	0.9410
HKYG	40	-2139.9592	4359.9184	0.0299	0.9709
HKYI	40	-2140.4567	4360.9134	0.0182	0.9890
HKYIG	41	-2139.9629	4361.9258	0.0110	1.0000
GTR	43	-2155.6753	4397.3507	0.0000	1.0000
HKY	39	-2163.8397	4405.6795	0.0000	1.0000
K2PG	37	-2166.9658	4407.9316	0.0000	1.0000
K2PI	37	-2167.1616	4408.3231	0.0000	1.0000
K2PIG	38	-2166.9657	4409.9313	0.0000	1.0000
SYMG	41	-2164.8578	4411.7156	0.0000	1.0000
SYMI	41	-2165.0438	4412.0875	0.0000	1.0000
SYMIG	42	-2164.8577	4413.7153	0.0000	1.0000
F81G	39	-2175.3501	4428.7002	0.0000	1.0000
F81I	39	-2175.7587	4429.5174	0.0000	1.0000
F81IG	40	-2175.3522	4430.7044	0.0000	1.0000
K2P	36	-2193.9553	4459.9105	0.0000	1.0000
SYM	40	-2190.8691	4461.7383	0.0000	1.0000
JC69G	36	-2199.5926	4471.1852	0.0000	1.0000
JC69I	36	-2199.8079	4471.6159	0.0000	1.0000
JC69IG	37	-2199.5990	4473.1980	0.0000	1.0000
F81	38	-2200.1279	4476.2558	0.0000	1.0000
JC69	35	-2226.0125	4522.0249	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2139.9592	4538.9973	0.6059	0.6059
HKYI	40	-2140.4567	4539.9923	0.3684	0.9743
HKYIG	41	-2139.9629	4545.4817	0.0237	0.9980
GTRG	44	-2133.0448	4551.0763	0.0014	0.9995
GTRI	44	-2134.1306	4553.2479	0.0005	0.9999
GTRIG	45	-2133.0408	4557.5453	0.0001	1.0000
K2PG	37	-2166.9658	4573.5796	0.0000	1.0000
K2PI	37	-2167.1616	4573.9711	0.0000	1.0000
K2PIG	38	-2166.9657	4580.0562	0.0000	1.0000
HKY	39	-2163.8397	4580.2814	0.0000	1.0000
GTR	43	-2155.6753	4589.8605	0.0000	1.0000
SYMG	41	-2164.8578	4595.2714	0.0000	1.0000
SYMI	41	-2165.0438	4595.6434	0.0000	1.0000
SYMIG	42	-2164.8577	4601.7482	0.0000	1.0000
F81G	39	-2175.3501	4603.3021	0.0000	1.0000
F81I	39	-2175.7587	4604.1193	0.0000	1.0000
F81IG	40	-2175.3522	4609.7833	0.0000	1.0000
K2P	36	-2193.9553	4621.0815	0.0000	1.0000
JC69G	36	-2199.5926	4632.3562	0.0000	1.0000
JC69I	36	-2199.8079	4632.7869	0.0000	1.0000
JC69IG	37	-2199.5990	4638.8460	0.0000	1.0000
SYM	40	-2190.8691	4640.8172	0.0000	1.0000
F81	38	-2200.1279	4646.3807	0.0000	1.0000
JC69	35	-2226.0125	4678.7189	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/chrZ_4723.phylip = 1 - 650;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4723.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/chrZ_4723.phylip = 1 - 650;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4723.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/chrZ_4723.phylip = 1 - 650;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4723.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

