
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:23 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/chr8_9158.phylip" (19 taxa, 620 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	-2048.8990	4192.6850	0.6043	0.6043
GTRIG	45	-2048.4196	4194.0517	0.3051	0.9093
GTRI	44	-2050.8069	4196.5008	0.0897	0.9990
SYMG	41	-2059.3678	4206.6941	0.0005	0.9996
SYMIG	42	-2059.1924	4208.6448	0.0002	0.9998
SYMI	41	-2060.5892	4209.1370	0.0002	0.9999
HKYG	40	-2062.9336	4211.5322	0.0000	1.0000
HKYIG	41	-2062.5137	4212.9858	0.0000	1.0000
HKYI	40	-2064.8194	4215.3037	0.0000	1.0000
K2PG	37	-2070.6265	4220.0845	0.0000	1.0000
K2PIG	38	-2070.3709	4221.8433	0.0000	1.0000
K2PI	37	-2072.1557	4223.1431	0.0000	1.0000
F81G	39	-2092.3893	4268.1579	0.0000	1.0000
F81IG	40	-2091.9955	4269.6559	0.0000	1.0000
JC69G	36	-2097.7749	4272.1192	0.0000	1.0000
F81I	39	-2094.4864	4272.3522	0.0000	1.0000
JC69IG	37	-2097.4513	4273.7343	0.0000	1.0000
JC69I	36	-2099.7000	4275.9695	0.0000	1.0000
GTR	43	-2097.4001	4287.3697	0.0000	1.0000
SYM	40	-2105.2944	4296.2538	0.0000	1.0000
HKY	39	-2109.2699	4301.9190	0.0000	1.0000
K2P	36	-2115.8564	4308.2823	0.0000	1.0000
F81	38	-2137.8024	4356.7063	0.0000	1.0000
JC69	35	-2142.7002	4359.7155	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2048.8990	4185.7980	0.5735	0.5735
GTRIG	45	-2048.4196	4186.8392	0.3408	0.9143
GTRI	44	-2050.8069	4189.6139	0.0851	0.9994
SYMG	41	-2059.3678	4200.7357	0.0003	0.9997
SYMIG	42	-2059.1924	4202.3848	0.0001	0.9999
SYMI	41	-2060.5892	4203.1785	0.0001	1.0000
HKYG	40	-2062.9336	4205.8672	0.0000	1.0000
HKYIG	41	-2062.5137	4207.0273	0.0000	1.0000
HKYI	40	-2064.8194	4209.6388	0.0000	1.0000
K2PG	37	-2070.6265	4215.2529	0.0000	1.0000
K2PIG	38	-2070.3709	4216.7417	0.0000	1.0000
K2PI	37	-2072.1557	4218.3114	0.0000	1.0000
F81G	39	-2092.3893	4262.7786	0.0000	1.0000
F81IG	40	-2091.9955	4263.9910	0.0000	1.0000
F81I	39	-2094.4864	4266.9729	0.0000	1.0000
JC69G	36	-2097.7749	4267.5498	0.0000	1.0000
JC69IG	37	-2097.4513	4268.9027	0.0000	1.0000
JC69I	36	-2099.7000	4271.4000	0.0000	1.0000
GTR	43	-2097.4001	4280.8003	0.0000	1.0000
SYM	40	-2105.2944	4290.5889	0.0000	1.0000
HKY	39	-2109.2699	4296.5397	0.0000	1.0000
K2P	36	-2115.8564	4303.7128	0.0000	1.0000
F81	38	-2137.8024	4351.6047	0.0000	1.0000
JC69	35	-2142.7002	4355.4004	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2070.6265	4379.1525	0.4406	0.4406
GTRG	44	-2048.8990	4380.7057	0.2027	0.6432
K2PI	37	-2072.1557	4382.2111	0.0955	0.7387
SYMG	41	-2059.3678	4382.3542	0.0889	0.8276
HKYG	40	-2062.9336	4383.0560	0.0626	0.8902
GTRI	44	-2050.8069	4384.5215	0.0301	0.9202
SYMI	41	-2060.5892	4384.7970	0.0262	0.9464
K2PIG	38	-2070.3709	4385.0711	0.0228	0.9693
GTRIG	45	-2048.4196	4386.1766	0.0131	0.9824
HKYI	40	-2064.8194	4386.8276	0.0095	0.9919
SYMIG	42	-2059.1924	4388.4330	0.0043	0.9962
HKYIG	41	-2062.5137	4388.6458	0.0038	1.0000
JC69G	36	-2097.7749	4427.0197	0.0000	1.0000
JC69I	36	-2099.7000	4430.8699	0.0000	1.0000
JC69IG	37	-2097.4513	4432.8023	0.0000	1.0000
F81G	39	-2092.3893	4435.5376	0.0000	1.0000
F81I	39	-2094.4864	4439.7319	0.0000	1.0000
F81IG	40	-2091.9955	4441.1798	0.0000	1.0000
K2P	36	-2115.8564	4463.1827	0.0000	1.0000
SYM	40	-2105.2944	4467.7777	0.0000	1.0000
HKY	39	-2109.2699	4469.2988	0.0000	1.0000
GTR	43	-2097.4001	4471.2782	0.0000	1.0000
JC69	35	-2142.7002	4510.4406	0.0000	1.0000
F81	38	-2137.8024	4519.9341	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/chr8_9158.phylip = 1 - 620;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_9158.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/chr8_9158.phylip = 1 - 620;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_9158.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/chr8_9158.phylip = 1 - 620;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_9158.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

