
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:41 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_3326.phylip" (19 taxa, 478 characters)

Minimum AIC  model: GTRG
Minimum AICc model: K2PG
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
K2PG	37	-1949.9588	3980.3085	0.2886	0.2886
GTRG	44	-1942.1003	3981.3461	0.1718	0.4604
HKYG	40	-1947.1910	3981.8878	0.1310	0.5914
GTRIG	45	-1941.2267	3982.0367	0.1216	0.7130
K2PIG	38	-1949.8143	3982.3803	0.1024	0.8154
GTRI	44	-1942.7746	3982.6947	0.0875	0.9029
HKYIG	41	-1946.9763	3983.8517	0.0491	0.9520
SYMG	41	-1947.5040	3984.9071	0.0290	0.9810
SYMIG	42	-1947.2199	3986.7432	0.0116	0.9925
K2PI	37	-1954.0985	3988.5879	0.0046	0.9971
HKYI	40	-1951.3106	3990.1269	0.0021	0.9993
SYMI	41	-1951.1593	3992.2177	0.0007	1.0000
K2P	36	-1993.8928	4065.8263	0.0000	1.0000
GTR	43	-1985.8994	4066.5176	0.0000	1.0000
HKY	39	-1990.9471	4067.0175	0.0000	1.0000
SYM	40	-1990.2811	4068.0679	0.0000	1.0000
F81G	39	-1992.9638	4071.0509	0.0000	1.0000
JC69G	36	-1996.6500	4071.3408	0.0000	1.0000
F81IG	40	-1992.8118	4073.1293	0.0000	1.0000
JC69IG	37	-1997.1505	4074.6919	0.0000	1.0000
F81I	39	-1995.7475	4076.6184	0.0000	1.0000
JC69I	36	-1999.5898	4077.2205	0.0000	1.0000
JC69	35	-2038.5327	4152.7668	0.0000	1.0000
F81	38	-2035.4869	4153.7255	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1942.1003	3972.2006	0.2753	0.2753
GTRIG	45	-1941.2267	3972.4534	0.2426	0.5178
GTRI	44	-1942.7746	3973.5492	0.1402	0.6581
K2PG	37	-1949.9588	3973.9176	0.1167	0.7747
HKYG	40	-1947.1910	3974.3821	0.0925	0.8672
K2PIG	38	-1949.8143	3975.6286	0.0496	0.9168
HKYIG	41	-1946.9763	3975.9526	0.0422	0.9590
SYMG	41	-1947.5040	3977.0080	0.0249	0.9838
SYMIG	42	-1947.2199	3978.4397	0.0122	0.9960
K2PI	37	-1954.0985	3982.1970	0.0019	0.9979
HKYI	40	-1951.3106	3982.6212	0.0015	0.9994
SYMI	41	-1951.1593	3984.3186	0.0006	1.0000
GTR	43	-1985.8994	4057.7987	0.0000	1.0000
K2P	36	-1993.8928	4059.7855	0.0000	1.0000
HKY	39	-1990.9471	4059.8943	0.0000	1.0000
SYM	40	-1990.2811	4060.5621	0.0000	1.0000
F81G	39	-1992.9638	4063.9276	0.0000	1.0000
JC69G	36	-1996.6500	4065.3000	0.0000	1.0000
F81IG	40	-1992.8118	4065.6236	0.0000	1.0000
JC69IG	37	-1997.1505	4068.3010	0.0000	1.0000
F81I	39	-1995.7475	4069.4951	0.0000	1.0000
JC69I	36	-1999.5898	4071.1796	0.0000	1.0000
F81	38	-2035.4869	4146.9738	0.0000	1.0000
JC69	35	-2038.5327	4147.0654	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1949.9588	4128.1932	0.9342	0.9342
K2PIG	38	-1949.8143	4134.0738	0.0494	0.9835
K2PI	37	-1954.0985	4136.4726	0.0149	0.9984
HKYG	40	-1947.1910	4141.1665	0.0014	0.9998
HKYIG	41	-1946.9763	4146.9067	0.0001	0.9999
SYMG	41	-1947.5040	4147.9620	0.0000	1.0000
HKYI	40	-1951.3106	4149.4056	0.0000	1.0000
SYMIG	42	-1947.2199	4153.5634	0.0000	1.0000
SYMI	41	-1951.1593	4155.2726	0.0000	1.0000
GTRG	44	-1942.1003	4155.6635	0.0000	1.0000
GTRI	44	-1942.7746	4157.0121	0.0000	1.0000
GTRIG	45	-1941.2267	4160.0859	0.0000	1.0000
K2P	36	-1993.8928	4209.8915	0.0000	1.0000
JC69G	36	-1996.6500	4215.4060	0.0000	1.0000
JC69I	36	-1999.5898	4221.2856	0.0000	1.0000
HKY	39	-1990.9471	4222.5091	0.0000	1.0000
JC69IG	37	-1997.1505	4222.5766	0.0000	1.0000
F81G	39	-1992.9638	4226.5424	0.0000	1.0000
SYM	40	-1990.2811	4227.3466	0.0000	1.0000
F81I	39	-1995.7475	4232.1099	0.0000	1.0000
F81IG	40	-1992.8118	4232.4080	0.0000	1.0000
GTR	43	-1985.8994	4237.0920	0.0000	1.0000
JC69	35	-2038.5327	4293.0018	0.0000	1.0000
F81	38	-2035.4869	4305.4190	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/chr6_3326.phylip = 1 - 478;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3326.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3326.phylip = 1 - 478;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3326.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;


[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/chr6_3326.phylip = 1 - 478;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3326.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

