
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:14 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/chr11_4886.phylip" (19 taxa, 617 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-2097.2204	4289.3638	0.9050	0.9050
HKYG	40	-2104.3924	4294.4793	0.0701	0.9751
GTRIG	45	-2099.8609	4296.9723	0.0202	0.9952
GTRI	44	-2103.1633	4301.2497	0.0024	0.9976
HKYIG	41	-2107.7825	4303.5545	0.0008	0.9984
K2PG	37	-2112.4637	4303.7839	0.0007	0.9990
K2PI	37	-2113.1073	4305.0713	0.0004	0.9994
HKYI	40	-2109.7495	4305.1935	0.0003	0.9997
SYMG	41	-2109.1129	4306.2154	0.0002	0.9999
SYMI	41	-2110.0062	4308.0019	0.0001	1.0000
K2PIG	38	-2116.5100	4314.1481	0.0000	1.0000
SYMIG	42	-2113.0382	4316.3691	0.0000	1.0000
F81G	39	-2154.8051	4393.0175	0.0000	1.0000
JC69G	36	-2161.5631	4399.7193	0.0000	1.0000
JC69I	36	-2162.3480	4401.2890	0.0000	1.0000
GTR	43	-2156.3768	4405.3574	0.0000	1.0000
F81IG	40	-2160.1835	4406.0614	0.0000	1.0000
HKY	39	-2162.0487	4407.5047	0.0000	1.0000
F81I	39	-2162.0596	4407.5264	0.0000	1.0000
JC69IG	37	-2167.4123	4413.6813	0.0000	1.0000
K2P	36	-2169.5278	4415.6487	0.0000	1.0000
SYM	40	-2166.5815	4418.8574	0.0000	1.0000
F81	38	-2210.7355	4502.5990	0.0000	1.0000
JC69	35	-2217.3832	4509.1037	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2097.2204	4282.4407	0.9328	0.9328
HKYG	40	-2104.3924	4288.7848	0.0391	0.9719
GTRIG	45	-2099.8609	4289.7219	0.0245	0.9963
GTRI	44	-2103.1633	4294.3266	0.0024	0.9988
HKYIG	41	-2107.7825	4297.5649	0.0005	0.9993
K2PG	37	-2112.4637	4298.9273	0.0002	0.9995
HKYI	40	-2109.7495	4299.4991	0.0002	0.9997
K2PI	37	-2113.1073	4300.2146	0.0001	0.9998
SYMG	41	-2109.1129	4300.2258	0.0001	0.9999
SYMI	41	-2110.0062	4302.0123	0.0001	1.0000
K2PIG	38	-2116.5100	4309.0201	0.0000	1.0000
SYMIG	42	-2113.0382	4310.0764	0.0000	1.0000
F81G	39	-2154.8051	4387.6102	0.0000	1.0000
JC69G	36	-2161.5631	4395.1262	0.0000	1.0000
JC69I	36	-2162.3480	4396.6959	0.0000	1.0000
GTR	43	-2156.3768	4398.7535	0.0000	1.0000
F81IG	40	-2160.1835	4400.3670	0.0000	1.0000
HKY	39	-2162.0487	4402.0974	0.0000	1.0000
F81I	39	-2162.0596	4402.1191	0.0000	1.0000
JC69IG	37	-2167.4123	4408.8247	0.0000	1.0000
K2P	36	-2169.5278	4411.0556	0.0000	1.0000
SYM	40	-2166.5815	4413.1630	0.0000	1.0000
F81	38	-2210.7355	4497.4710	0.0000	1.0000
JC69	35	-2217.3832	4504.7664	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2112.4637	4462.6475	0.5757	0.5757
K2PI	37	-2113.1073	4463.9348	0.3025	0.8781
HKYG	40	-2104.3924	4465.7796	0.1202	0.9984
HKYI	40	-2109.7495	4476.4939	0.0006	0.9990
GTRG	44	-2097.2204	4477.1350	0.0004	0.9994
K2PIG	38	-2116.5100	4477.1651	0.0004	0.9998
HKYIG	41	-2107.7825	4478.9846	0.0002	0.9999
SYMG	41	-2109.1129	4481.6454	0.0000	1.0000
SYMI	41	-2110.0062	4483.4320	0.0000	1.0000
GTRIG	45	-2099.8609	4488.8410	0.0000	1.0000
GTRI	44	-2103.1633	4489.0208	0.0000	1.0000
SYMIG	42	-2113.0382	4495.9209	0.0000	1.0000
JC69G	36	-2161.5631	4554.4215	0.0000	1.0000
JC69I	36	-2162.3480	4555.9912	0.0000	1.0000
F81G	39	-2154.8051	4560.1801	0.0000	1.0000
K2P	36	-2169.5278	4570.3509	0.0000	1.0000
JC69IG	37	-2167.4123	4572.5448	0.0000	1.0000
HKY	39	-2162.0487	4574.6673	0.0000	1.0000
F81I	39	-2162.0596	4574.6890	0.0000	1.0000
F81IG	40	-2160.1835	4577.3617	0.0000	1.0000
GTR	43	-2156.3768	4589.0229	0.0000	1.0000
SYM	40	-2166.5815	4590.1577	0.0000	1.0000
JC69	35	-2217.3832	4659.6368	0.0000	1.0000
F81	38	-2210.7355	4665.6160	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/chr11_4886.phylip = 1 - 617;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4886.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/chr11_4886.phylip = 1 - 617;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4886.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4886.phylip = 1 - 617;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4886.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

