
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:33 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/chr9_5190.phylip" (19 taxa, 706 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-2048.4027	4190.7963	0.6419	0.6419
GTRIG	45	-2048.1838	4192.6403	0.2553	0.8973
GTRI	44	-2050.2371	4194.4652	0.1025	0.9998
HKYG	40	-2061.4297	4207.7916	0.0001	0.9999
HKYIG	41	-2061.1656	4209.5180	0.0001	1.0000
HKYI	40	-2062.8130	4210.5584	0.0000	1.0000
GTR	43	-2077.2212	4246.1584	0.0000	1.0000
HKY	39	-2089.1309	4260.9465	0.0000	1.0000
SYMG	41	-2087.1222	4261.4311	0.0000	1.0000
K2PG	37	-2092.1609	4262.5315	0.0000	1.0000
SYMIG	42	-2086.9358	4263.3196	0.0000	1.0000
SYMI	41	-2088.1203	4263.4273	0.0000	1.0000
K2PI	37	-2093.0579	4264.3254	0.0000	1.0000
K2PIG	38	-2092.3135	4265.0707	0.0000	1.0000
F81G	39	-2104.9196	4292.5238	0.0000	1.0000
F81I	39	-2105.8086	4294.3018	0.0000	1.0000
F81IG	40	-2104.9913	4294.9150	0.0000	1.0000
SYM	40	-2114.3501	4313.6325	0.0000	1.0000
K2P	36	-2120.0750	4316.1320	0.0000	1.0000
JC69G	36	-2131.3065	4338.5950	0.0000	1.0000
JC69I	36	-2132.1184	4340.2188	0.0000	1.0000
JC69IG	37	-2131.1568	4340.5231	0.0000	1.0000
F81	38	-2131.4851	4343.4139	0.0000	1.0000
JC69	35	-2158.2062	4390.1736	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2048.4027	4184.8054	0.6181	0.6181
GTRIG	45	-2048.1838	4186.3676	0.2830	0.9012
GTRI	44	-2050.2371	4188.4742	0.0987	0.9999
HKYG	40	-2061.4297	4202.8593	0.0001	0.9999
HKYIG	41	-2061.1656	4204.3312	0.0000	1.0000
HKYI	40	-2062.8130	4205.6261	0.0000	1.0000
GTR	43	-2077.2212	4240.4424	0.0000	1.0000
SYMG	41	-2087.1222	4256.2444	0.0000	1.0000
HKY	39	-2089.1309	4256.2619	0.0000	1.0000
SYMIG	42	-2086.9358	4257.8717	0.0000	1.0000
SYMI	41	-2088.1203	4258.2406	0.0000	1.0000
K2PG	37	-2092.1609	4258.3219	0.0000	1.0000
K2PI	37	-2093.0579	4260.1158	0.0000	1.0000
K2PIG	38	-2092.3135	4260.6269	0.0000	1.0000
F81G	39	-2104.9196	4287.8391	0.0000	1.0000
F81I	39	-2105.8086	4289.6172	0.0000	1.0000
F81IG	40	-2104.9913	4289.9827	0.0000	1.0000
SYM	40	-2114.3501	4308.7002	0.0000	1.0000
K2P	36	-2120.0750	4312.1499	0.0000	1.0000
JC69G	36	-2131.3065	4334.6129	0.0000	1.0000
JC69I	36	-2132.1184	4336.2367	0.0000	1.0000
JC69IG	37	-2131.1568	4336.3135	0.0000	1.0000
F81	38	-2131.4851	4338.9701	0.0000	1.0000
JC69	35	-2158.2062	4386.4124	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2061.4297	4385.2439	0.4167	0.4167
GTRG	44	-2048.4027	4385.4284	0.3800	0.7966
HKYI	40	-2062.8130	4388.0107	0.1045	0.9011
GTRI	44	-2050.2371	4389.0973	0.0607	0.9618
HKYIG	41	-2061.1656	4391.2755	0.0204	0.9822
GTRIG	45	-2048.1838	4391.5503	0.0178	1.0000
K2PG	37	-2092.1609	4427.0277	0.0000	1.0000
K2PI	37	-2093.0579	4428.8216	0.0000	1.0000
K2PIG	38	-2092.3135	4433.8923	0.0000	1.0000
HKY	39	-2089.1309	4434.0869	0.0000	1.0000
GTR	43	-2077.2212	4436.5058	0.0000	1.0000
SYMG	41	-2087.1222	4443.1886	0.0000	1.0000
SYMI	41	-2088.1203	4445.1848	0.0000	1.0000
SYMIG	42	-2086.9358	4449.3755	0.0000	1.0000
F81G	39	-2104.9196	4465.6641	0.0000	1.0000
F81I	39	-2105.8086	4467.4422	0.0000	1.0000
F81IG	40	-2104.9913	4472.3673	0.0000	1.0000
K2P	36	-2120.0750	4476.2961	0.0000	1.0000
SYM	40	-2114.3501	4491.0848	0.0000	1.0000
JC69G	36	-2131.3065	4498.7590	0.0000	1.0000
JC69I	36	-2132.1184	4500.3829	0.0000	1.0000
JC69IG	37	-2131.1568	4505.0193	0.0000	1.0000
F81	38	-2131.4851	4512.2355	0.0000	1.0000
JC69	35	-2158.2062	4545.9990	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/chr9_5190.phylip = 1 - 706;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5190.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/chr9_5190.phylip = 1 - 706;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5190.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5190.phylip = 1 - 706;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5190.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

