
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:51 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/chr2_20206.phylip" (19 taxa, 508 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	-2038.4643	4173.4816	0.3429	0.3429
GTRIG	45	-2037.6251	4174.2111	0.2381	0.5810
HKYG	40	-2043.7665	4174.5566	0.2003	0.7814
HKYIG	41	-2043.1504	4175.6914	0.1136	0.8949
GTRI	44	-2040.1499	4176.8527	0.0636	0.9585
HKYI	40	-2045.3728	4177.7691	0.0402	0.9987
K2PG	37	-2052.9927	4185.9685	0.0007	0.9994
K2PIG	38	-2052.2780	4186.8758	0.0004	0.9998
K2PI	37	-2054.6386	4189.2603	0.0001	0.9999
SYMG	41	-2050.8205	4191.0315	0.0001	1.0000
SYMIG	42	-2050.1571	4192.0819	0.0000	1.0000
SYMI	41	-2053.2394	4195.8694	0.0000	1.0000
GTR	43	-2074.4634	4243.0819	0.0000	1.0000
HKY	39	-2079.5762	4243.8191	0.0000	1.0000
K2P	36	-2088.4958	4254.6477	0.0000	1.0000
SYM	40	-2086.4216	4259.8668	0.0000	1.0000
F81G	39	-2106.0736	4296.8140	0.0000	1.0000
F81IG	40	-2105.0682	4297.1599	0.0000	1.0000
F81I	39	-2107.4554	4299.5774	0.0000	1.0000
JC69G	36	-2113.1689	4303.9939	0.0000	1.0000
JC69IG	37	-2112.1635	4304.3100	0.0000	1.0000
JC69I	36	-2114.6360	4306.9281	0.0000	1.0000
F81	38	-2139.9420	4362.2038	0.0000	1.0000
JC69	35	-2147.3136	4369.9661	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2038.4643	4164.9287	0.3922	0.3922
GTRIG	45	-2037.6251	4165.2501	0.3340	0.7261
HKYG	40	-2043.7665	4167.5331	0.1066	0.8328
GTRI	44	-2040.1499	4168.2997	0.0727	0.9055
HKYIG	41	-2043.1504	4168.3009	0.0726	0.9781
HKYI	40	-2045.3728	4170.7456	0.0214	0.9995
K2PG	37	-2052.9927	4179.9855	0.0002	0.9997
K2PIG	38	-2052.2780	4180.5560	0.0002	0.9999
K2PI	37	-2054.6386	4183.2773	0.0000	0.9999
SYMG	41	-2050.8205	4183.6409	0.0000	1.0000
SYMIG	42	-2050.1571	4184.3141	0.0000	1.0000
SYMI	41	-2053.2394	4188.4789	0.0000	1.0000
GTR	43	-2074.4634	4234.9267	0.0000	1.0000
HKY	39	-2079.5762	4237.1525	0.0000	1.0000
K2P	36	-2088.4958	4248.9917	0.0000	1.0000
SYM	40	-2086.4216	4252.8433	0.0000	1.0000
F81IG	40	-2105.0682	4290.1364	0.0000	1.0000
F81G	39	-2106.0736	4290.1473	0.0000	1.0000
F81I	39	-2107.4554	4292.9107	0.0000	1.0000
JC69IG	37	-2112.1635	4298.3271	0.0000	1.0000
JC69G	36	-2113.1689	4298.3379	0.0000	1.0000
JC69I	36	-2114.6360	4301.2720	0.0000	1.0000
F81	38	-2139.9420	4355.8840	0.0000	1.0000
JC69	35	-2147.3136	4364.6272	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2052.9927	4336.5133	0.4128	0.4128
HKYG	40	-2043.7665	4336.7523	0.3663	0.7790
K2PI	37	-2054.6386	4339.8051	0.0796	0.8586
HKYI	40	-2045.3728	4339.9648	0.0735	0.9321
K2PIG	38	-2052.2780	4341.3143	0.0374	0.9695
HKYIG	41	-2043.1504	4341.7506	0.0301	0.9996
GTRG	44	-2038.4643	4351.0698	0.0003	0.9999
GTRI	44	-2040.1499	4354.4409	0.0001	1.0000
GTRIG	45	-2037.6251	4355.6218	0.0000	1.0000
SYMG	41	-2050.8205	4357.0906	0.0000	1.0000
SYMI	41	-2053.2394	4361.9286	0.0000	1.0000
SYMIG	42	-2050.1571	4361.9943	0.0000	1.0000
K2P	36	-2088.4958	4401.2890	0.0000	1.0000
HKY	39	-2079.5762	4402.1412	0.0000	1.0000
GTR	43	-2074.4634	4416.8374	0.0000	1.0000
SYM	40	-2086.4216	4422.0625	0.0000	1.0000
JC69G	36	-2113.1689	4450.6352	0.0000	1.0000
JC69I	36	-2114.6360	4453.5693	0.0000	1.0000
JC69IG	37	-2112.1635	4454.8549	0.0000	1.0000
F81G	39	-2106.0736	4455.1361	0.0000	1.0000
F81I	39	-2107.4554	4457.8995	0.0000	1.0000
F81IG	40	-2105.0682	4459.3556	0.0000	1.0000
JC69	35	-2147.3136	4512.6940	0.0000	1.0000
F81	38	-2139.9420	4516.6423	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/chr2_20206.phylip = 1 - 508;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_20206.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/chr2_20206.phylip = 1 - 508;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_20206.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/chr2_20206.phylip = 1 - 508;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_20206.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;


-------------------------------------------------------------
End of Output

