
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:06 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_6644.phylip" (19 taxa, 594 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
Minimum BIC  model: HKYIG


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
HKYIG	41	-2032.9182	4154.0756	0.7034	0.7034
GTRIG	45	-2029.1876	4155.9300	0.2783	0.9816
HKYG	40	-2038.0733	4162.0780	0.0129	0.9945
GTRG	44	-2034.3736	4163.9604	0.0050	0.9995
HKYI	40	-2041.7111	4169.3535	0.0003	0.9999
GTRI	44	-2037.9912	4171.1955	0.0001	1.0000
K2PIG	38	-2051.9353	4185.2111	0.0000	1.0000
SYMIG	42	-2047.7594	4186.0741	0.0000	1.0000
K2PG	37	-2055.6511	4190.3598	0.0000	1.0000
SYMG	41	-2051.3347	4190.9085	0.0000	1.0000
SYMI	41	-2053.6761	4195.5914	0.0000	1.0000
K2PI	37	-2058.3638	4195.7852	0.0000	1.0000
F81IG	40	-2092.4214	4270.7740	0.0000	1.0000
F81G	39	-2095.9927	4275.6173	0.0000	1.0000
F81I	39	-2098.9765	4281.5847	0.0000	1.0000
JC69IG	37	-2105.6097	4290.2770	0.0000	1.0000
JC69G	36	-2108.6768	4294.1365	0.0000	1.0000
JC69I	36	-2111.2177	4299.2181	0.0000	1.0000
HKY	39	-2134.0175	4351.6668	0.0000	1.0000
GTR	43	-2129.8226	4352.5253	0.0000	1.0000
K2P	36	-2148.4595	4373.7017	0.0000	1.0000
SYM	40	-2144.2418	4374.4149	0.0000	1.0000
F81	38	-2185.5653	4452.4712	0.0000	1.0000
JC69	35	-2197.6699	4469.8559	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-2032.9182	4147.8364	0.5581	0.5581
GTRIG	45	-2029.1876	4148.3752	0.4263	0.9844
HKYG	40	-2038.0733	4156.1467	0.0088	0.9931
GTRG	44	-2034.3736	4156.7473	0.0065	0.9996
HKYI	40	-2041.7111	4163.4222	0.0002	0.9998
GTRI	44	-2037.9912	4163.9824	0.0002	1.0000
SYMIG	42	-2047.7594	4179.5188	0.0000	1.0000
K2PIG	38	-2051.9353	4179.8706	0.0000	1.0000
SYMG	41	-2051.3347	4184.6693	0.0000	1.0000
K2PG	37	-2055.6511	4185.3022	0.0000	1.0000
SYMI	41	-2053.6761	4189.3523	0.0000	1.0000
K2PI	37	-2058.3638	4190.7277	0.0000	1.0000
F81IG	40	-2092.4214	4264.8427	0.0000	1.0000
F81G	39	-2095.9927	4269.9855	0.0000	1.0000
F81I	39	-2098.9765	4275.9530	0.0000	1.0000
JC69IG	37	-2105.6097	4285.2194	0.0000	1.0000
JC69G	36	-2108.6768	4289.3537	0.0000	1.0000
JC69I	36	-2111.2177	4294.4353	0.0000	1.0000
GTR	43	-2129.8226	4345.6453	0.0000	1.0000
HKY	39	-2134.0175	4346.0351	0.0000	1.0000
SYM	40	-2144.2418	4368.4837	0.0000	1.0000
K2P	36	-2148.4595	4368.9189	0.0000	1.0000
F81	38	-2185.5653	4447.1307	0.0000	1.0000
JC69	35	-2197.6699	4465.3398	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYIG	41	-2032.9182	4327.6985	0.8737	0.8737
HKYG	40	-2038.0733	4331.6219	0.1229	0.9965
HKYI	40	-2041.7111	4338.8974	0.0032	0.9998
GTRIG	45	-2029.1876	4345.7848	0.0001	0.9999
K2PIG	38	-2051.9353	4346.5720	0.0001	0.9999
K2PG	37	-2055.6511	4347.6167	0.0000	1.0000
GTRG	44	-2034.3736	4349.7700	0.0000	1.0000
K2PI	37	-2058.3638	4353.0422	0.0000	1.0000
GTRI	44	-2037.9912	4357.0051	0.0000	1.0000
SYMIG	42	-2047.7594	4363.7677	0.0000	1.0000
SYMG	41	-2051.3347	4364.5314	0.0000	1.0000
SYMI	41	-2053.6761	4369.2143	0.0000	1.0000
F81IG	40	-2092.4214	4440.3179	0.0000	1.0000
F81G	39	-2095.9927	4441.0738	0.0000	1.0000
F81I	39	-2098.9765	4447.0413	0.0000	1.0000
JC69G	36	-2108.6768	4447.2814	0.0000	1.0000
JC69IG	37	-2105.6097	4447.5340	0.0000	1.0000
JC69I	36	-2111.2177	4452.3630	0.0000	1.0000
HKY	39	-2134.0175	4517.1234	0.0000	1.0000
K2P	36	-2148.4595	4526.8466	0.0000	1.0000
GTR	43	-2129.8226	4534.2811	0.0000	1.0000
SYM	40	-2144.2418	4543.9588	0.0000	1.0000
F81	38	-2185.5653	4613.8321	0.0000	1.0000
JC69	35	-2197.6699	4618.8806	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6644.phylip = 1 - 594;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6644.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6644.phylip = 1 - 594;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6644.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6644.phylip = 1 - 594;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6644.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

