
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:32 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/chr6_8786.phylip" (19 taxa, 611 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	-1919.0101	3923.7745	0.5533	0.5533
HKYIG	41	-1919.0036	3926.0598	0.1765	0.7297
HKYI	40	-1920.5777	3926.9098	0.1154	0.8451
GTRG	44	-1916.0429	3927.0822	0.1058	0.9510
GTRIG	45	-1916.0342	3929.3958	0.0333	0.9843
GTRI	44	-1917.9522	3930.9009	0.0157	0.9999
HKY	39	-1929.3333	3942.1307	0.0001	1.0000
GTR	43	-1927.1789	3947.0316	0.0000	1.0000
F81G	39	-1956.8633	3997.1907	0.0000	1.0000
F81IG	40	-1956.8664	3999.4871	0.0000	1.0000
F81I	39	-1958.1932	3999.8505	0.0000	1.0000
F81	38	-1965.4867	4012.1553	0.0000	1.0000
K2PG	37	-1973.0969	4025.1013	0.0000	1.0000
K2PI	37	-1974.1983	4027.3040	0.0000	1.0000
K2PIG	38	-1973.0958	4027.3735	0.0000	1.0000
SYMG	41	-1972.1049	4032.2626	0.0000	1.0000
SYMI	41	-1973.1723	4034.3974	0.0000	1.0000
SYMIG	42	-1972.1026	4034.5643	0.0000	1.0000
K2P	36	-1982.4235	4041.4881	0.0000	1.0000
SYM	40	-1981.6496	4049.0535	0.0000	1.0000
JC69G	36	-2001.3719	4079.3849	0.0000	1.0000
JC69IG	37	-2001.3728	4081.6531	0.0000	1.0000
JC69I	36	-2002.5153	4081.6716	0.0000	1.0000
JC69	35	-2009.8466	4094.0758	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1919.0101	3918.0201	0.4717	0.4717
HKYIG	41	-1919.0036	3920.0071	0.1747	0.6464
GTRG	44	-1916.0429	3920.0858	0.1679	0.8144
HKYI	40	-1920.5777	3921.1554	0.0984	0.9127
GTRIG	45	-1916.0342	3922.0684	0.0623	0.9751
GTRI	44	-1917.9522	3923.9044	0.0249	1.0000
HKY	39	-1929.3333	3936.6666	0.0000	1.0000
GTR	43	-1927.1789	3940.3579	0.0000	1.0000
F81G	39	-1956.8633	3991.7266	0.0000	1.0000
F81IG	40	-1956.8664	3993.7327	0.0000	1.0000
F81I	39	-1958.1932	3994.3864	0.0000	1.0000
F81	38	-1965.4867	4006.9735	0.0000	1.0000
K2PG	37	-1973.0969	4020.1938	0.0000	1.0000
K2PIG	38	-1973.0958	4022.1917	0.0000	1.0000
K2PI	37	-1974.1983	4022.3965	0.0000	1.0000
SYMG	41	-1972.1049	4026.2099	0.0000	1.0000
SYMIG	42	-1972.1026	4028.2052	0.0000	1.0000
SYMI	41	-1973.1723	4028.3447	0.0000	1.0000
K2P	36	-1982.4235	4036.8470	0.0000	1.0000
SYM	40	-1981.6496	4043.2991	0.0000	1.0000
JC69G	36	-2001.3719	4074.7438	0.0000	1.0000
JC69IG	37	-2001.3728	4076.7456	0.0000	1.0000
JC69I	36	-2002.5153	4077.0305	0.0000	1.0000
JC69	35	-2009.8466	4089.6932	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1919.0101	4094.6240	0.7999	0.7999
HKYI	40	-1920.5777	4097.7593	0.1668	0.9667
HKYIG	41	-1919.0036	4101.0261	0.0326	0.9993
HKY	39	-1929.3333	4108.8553	0.0006	1.0000
GTRG	44	-1916.0429	4114.3500	0.0000	1.0000
GTRI	44	-1917.9522	4118.1687	0.0000	1.0000
GTRIG	45	-1916.0342	4120.7478	0.0000	1.0000
GTR	43	-1927.1789	4130.2071	0.0000	1.0000
F81G	39	-1956.8633	4163.9153	0.0000	1.0000
F81I	39	-1958.1932	4166.5752	0.0000	1.0000
F81IG	40	-1956.8664	4170.3366	0.0000	1.0000
F81	38	-1965.4867	4174.7471	0.0000	1.0000
K2PG	37	-1973.0969	4183.5524	0.0000	1.0000
K2PI	37	-1974.1983	4185.7551	0.0000	1.0000
K2PIG	38	-1973.0958	4189.9653	0.0000	1.0000
K2P	36	-1982.4235	4195.7905	0.0000	1.0000
SYMG	41	-1972.1049	4207.2288	0.0000	1.0000
SYMI	41	-1973.1723	4209.3637	0.0000	1.0000
SYMIG	42	-1972.1026	4213.6393	0.0000	1.0000
SYM	40	-1981.6496	4219.9030	0.0000	1.0000
JC69G	36	-2001.3719	4233.6873	0.0000	1.0000
JC69I	36	-2002.5153	4235.9740	0.0000	1.0000
JC69IG	37	-2001.3728	4240.1042	0.0000	1.0000
JC69	35	-2009.8466	4244.2216	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/chr6_8786.phylip = 1 - 611;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8786.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/chr6_8786.phylip = 1 - 611;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8786.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/chr6_8786.phylip = 1 - 611;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8786.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

