
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:27 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_4926.phylip" (19 taxa, 526 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
Minimum BIC  model: HKYI


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
GTRI	44	-1917.6451	3931.5229	0.4335	0.4335
GTRG	44	-1917.7038	3931.6404	0.4087	0.8422
GTRIG	45	-1917.5131	3933.6513	0.1496	0.9918
HKYI	40	-1927.0463	3940.8555	0.0041	0.9958
HKYG	40	-1927.3971	3941.5572	0.0029	0.9987
HKYIG	41	-1927.0177	3943.1512	0.0013	1.0000
GTR	43	-1941.4582	3976.7670	0.0000	1.0000
HKY	39	-1950.4396	3985.2989	0.0000	1.0000
K2PI	37	-1956.4795	3992.7212	0.0000	1.0000
K2PG	37	-1956.6987	3993.1597	0.0000	1.0000
SYMI	41	-1952.3239	3993.7634	0.0000	1.0000
K2PIG	38	-1956.4064	3994.8990	0.0000	1.0000
SYMG	41	-1953.3952	3995.9062	0.0000	1.0000
SYMIG	42	-1952.2752	3996.0288	0.0000	1.0000
K2P	36	-1982.2520	4041.9519	0.0000	1.0000
SYM	40	-1978.1842	4043.1313	0.0000	1.0000
F81I	39	-1985.2923	4055.0044	0.0000	1.0000
F81G	39	-1985.3838	4055.1873	0.0000	1.0000
F81IG	40	-1985.1829	4057.1287	0.0000	1.0000
JC69I	36	-2007.3303	4092.1085	0.0000	1.0000
JC69G	36	-2008.3372	4094.1223	0.0000	1.0000
JC69IG	37	-2007.1942	4094.1506	0.0000	1.0000
F81	38	-2008.5927	4099.2717	0.0000	1.0000
JC69	35	-2032.4781	4140.0990	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1917.6451	3923.2901	0.4216	0.4216
GTRG	44	-1917.7038	3923.4076	0.3975	0.8191
GTRIG	45	-1917.5131	3925.0263	0.1770	0.9960
HKYI	40	-1927.0463	3934.0926	0.0019	0.9979
HKYG	40	-1927.3971	3934.7943	0.0013	0.9993
HKYIG	41	-1927.0177	3936.0355	0.0007	1.0000
GTR	43	-1941.4582	3968.9164	0.0000	1.0000
HKY	39	-1950.4396	3978.8791	0.0000	1.0000
SYMI	41	-1952.3239	3986.6477	0.0000	1.0000
K2PI	37	-1956.4795	3986.9589	0.0000	1.0000
K2PG	37	-1956.6987	3987.3974	0.0000	1.0000
SYMIG	42	-1952.2752	3988.5505	0.0000	1.0000
SYMG	41	-1953.3952	3988.7905	0.0000	1.0000
K2PIG	38	-1956.4064	3988.8127	0.0000	1.0000
SYM	40	-1978.1842	4036.3685	0.0000	1.0000
K2P	36	-1982.2520	4036.5040	0.0000	1.0000
F81I	39	-1985.2923	4048.5846	0.0000	1.0000
F81G	39	-1985.3838	4048.7675	0.0000	1.0000
F81IG	40	-1985.1829	4050.3658	0.0000	1.0000
JC69I	36	-2007.3303	4086.6607	0.0000	1.0000
JC69IG	37	-2007.1942	4088.3883	0.0000	1.0000
JC69G	36	-2008.3372	4088.6744	0.0000	1.0000
F81	38	-2008.5927	4093.1855	0.0000	1.0000
JC69	35	-2032.4781	4134.9561	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1927.0463	4104.7047	0.5446	0.5446
HKYG	40	-1927.3971	4105.4063	0.3835	0.9281
HKYIG	41	-1927.0177	4110.9128	0.0244	0.9525
GTRI	44	-1917.6451	4110.9634	0.0238	0.9763
GTRG	44	-1917.7038	4111.0809	0.0225	0.9988
GTRIG	45	-1917.5131	4116.9648	0.0012	1.0000
K2PI	37	-1956.4795	4144.7751	0.0000	1.0000
K2PG	37	-1956.6987	4145.2135	0.0000	1.0000
HKY	39	-1950.4396	4145.2259	0.0000	1.0000
K2PIG	38	-1956.4064	4150.8942	0.0000	1.0000
GTR	43	-1941.4582	4152.3244	0.0000	1.0000
SYMI	41	-1952.3239	4161.5251	0.0000	1.0000
SYMG	41	-1953.3952	4163.6678	0.0000	1.0000
SYMIG	42	-1952.2752	4167.6932	0.0000	1.0000
K2P	36	-1982.2520	4190.0549	0.0000	1.0000
SYM	40	-1978.1842	4206.9805	0.0000	1.0000
F81I	39	-1985.2923	4214.9314	0.0000	1.0000
F81G	39	-1985.3838	4215.1143	0.0000	1.0000
F81IG	40	-1985.1829	4220.9778	0.0000	1.0000
JC69I	36	-2007.3303	4240.2115	0.0000	1.0000
JC69G	36	-2008.3372	4242.2253	0.0000	1.0000
JC69IG	37	-2007.1942	4246.2044	0.0000	1.0000
F81	38	-2008.5927	4255.2669	0.0000	1.0000
JC69	35	-2032.4781	4284.2417	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_4926.phylip = 1 - 526;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_4926.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_4926.phylip = 1 - 526;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_4926.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_4926.phylip = 1 - 526;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_4926.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

