
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:19 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/chrZ_11479.phylip" (19 taxa, 692 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	-2049.5188	4184.0760	0.4384	0.4384
HKYI	40	-2050.2534	4185.5452	0.2103	0.6486
HKYIG	41	-2049.5096	4186.3178	0.1429	0.7915
GTRG	44	-2046.2826	4186.6857	0.1189	0.9104
GTRI	44	-2047.1211	4188.3628	0.0514	0.9618
GTRIG	45	-2046.2744	4188.9574	0.0382	1.0000
HKY	39	-2061.2172	4205.2197	0.0000	1.0000
GTR	43	-2057.8885	4207.6165	0.0000	1.0000
K2PG	37	-2070.5441	4219.3879	0.0000	1.0000
K2PI	37	-2071.2769	4220.8536	0.0000	1.0000
K2PIG	38	-2070.5286	4221.5962	0.0000	1.0000
SYMG	41	-2071.7543	4230.8071	0.0000	1.0000
SYMI	41	-2072.5961	4232.4907	0.0000	1.0000
SYMIG	42	-2071.7379	4233.0414	0.0000	1.0000
K2P	36	-2082.9009	4241.8689	0.0000	1.0000
SYM	40	-2083.8952	4252.8288	0.0000	1.0000
F81G	39	-2090.5021	4263.7895	0.0000	1.0000
F81I	39	-2091.1280	4265.0413	0.0000	1.0000
F81IG	40	-2090.5025	4266.0434	0.0000	1.0000
F81	38	-2101.2959	4283.1308	0.0000	1.0000
JC69G	36	-2110.1925	4296.4522	0.0000	1.0000
JC69I	36	-2110.8516	4297.7704	0.0000	1.0000
JC69IG	37	-2110.1899	4298.6796	0.0000	1.0000
JC69	35	-2121.4216	4316.6847	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-2049.5188	4179.0376	0.3716	0.3716
HKYI	40	-2050.2534	4180.5068	0.1782	0.5498
GTRG	44	-2046.2826	4180.5652	0.1731	0.7230
HKYIG	41	-2049.5096	4181.0193	0.1380	0.8609
GTRI	44	-2047.1211	4182.2422	0.0749	0.9358
GTRIG	45	-2046.2744	4182.5487	0.0642	1.0000
HKY	39	-2061.2172	4200.4345	0.0000	1.0000
GTR	43	-2057.8885	4201.7770	0.0000	1.0000
K2PG	37	-2070.5441	4215.0882	0.0000	1.0000
K2PI	37	-2071.2769	4216.5539	0.0000	1.0000
K2PIG	38	-2070.5286	4217.0571	0.0000	1.0000
SYMG	41	-2071.7543	4225.5086	0.0000	1.0000
SYMI	41	-2072.5961	4227.1923	0.0000	1.0000
SYMIG	42	-2071.7379	4227.4759	0.0000	1.0000
K2P	36	-2082.9009	4237.8017	0.0000	1.0000
SYM	40	-2083.8952	4247.7904	0.0000	1.0000
F81G	39	-2090.5021	4259.0042	0.0000	1.0000
F81I	39	-2091.1280	4260.2561	0.0000	1.0000
F81IG	40	-2090.5025	4261.0050	0.0000	1.0000
F81	38	-2101.2959	4278.5918	0.0000	1.0000
JC69G	36	-2110.1925	4292.3850	0.0000	1.0000
JC69I	36	-2110.8516	4293.7033	0.0000	1.0000
JC69IG	37	-2110.1899	4294.3799	0.0000	1.0000
JC69	35	-2121.4216	4312.8433	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2049.5188	4360.6210	0.6586	0.6586
HKYI	40	-2050.2534	4362.0903	0.3159	0.9745
HKYIG	41	-2049.5096	4367.1423	0.0253	0.9998
HKY	39	-2061.2172	4377.4783	0.0001	0.9999
GTRG	44	-2046.2826	4380.3070	0.0000	1.0000
GTRI	44	-2047.1211	4381.9840	0.0000	1.0000
K2PG	37	-2070.5441	4383.0528	0.0000	1.0000
K2PI	37	-2071.2769	4384.5186	0.0000	1.0000
GTRIG	45	-2046.2744	4386.8301	0.0000	1.0000
K2PIG	38	-2070.5286	4389.5614	0.0000	1.0000
GTR	43	-2057.8885	4396.9792	0.0000	1.0000
K2P	36	-2082.9009	4401.2268	0.0000	1.0000
SYMG	41	-2071.7543	4411.6316	0.0000	1.0000
SYMI	41	-2072.5961	4413.3153	0.0000	1.0000
SYMIG	42	-2071.7379	4418.1385	0.0000	1.0000
SYM	40	-2083.8952	4429.3738	0.0000	1.0000
F81G	39	-2090.5021	4436.0481	0.0000	1.0000
F81I	39	-2091.1280	4437.2999	0.0000	1.0000
F81IG	40	-2090.5025	4442.5885	0.0000	1.0000
F81	38	-2101.2959	4451.0960	0.0000	1.0000
JC69G	36	-2110.1925	4455.8101	0.0000	1.0000
JC69I	36	-2110.8516	4457.1284	0.0000	1.0000
JC69IG	37	-2110.1899	4462.3446	0.0000	1.0000
JC69	35	-2121.4216	4471.7288	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/chrZ_11479.phylip = 1 - 692;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11479.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/chrZ_11479.phylip = 1 - 692;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11479.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/chrZ_11479.phylip = 1 - 692;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11479.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

