
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:43 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/chr13_187.phylip" (19 taxa, 474 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	-1893.4798	3884.1904	0.7561	0.7561
GTRIG	45	-1893.4115	3886.4958	0.2388	0.9949
HKYG	40	-1904.2253	3896.0256	0.0020	0.9969
GTRI	44	-1899.6805	3896.5917	0.0015	0.9984
HKYIG	41	-1903.6112	3897.1946	0.0011	0.9996
HKYI	40	-1905.7643	3899.1036	0.0004	1.0000
GTR	43	-1911.4483	3917.6967	0.0000	1.0000
HKY	39	-1917.2647	3919.7183	0.0000	1.0000
SYMG	41	-1941.8835	3973.7392	0.0000	1.0000
K2PG	37	-1950.3538	3981.1572	0.0000	1.0000
SYMIG	42	-1945.6772	3983.7348	0.0000	1.0000
SYMI	41	-1947.0345	3984.0413	0.0000	1.0000
F81G	39	-1949.9346	3985.0581	0.0000	1.0000
K2PIG	38	-1954.2522	3991.3183	0.0000	1.0000
K2PI	37	-1956.1297	3992.7089	0.0000	1.0000
F81IG	40	-1955.7962	3999.1674	0.0000	1.0000
F81I	39	-1957.8448	4000.8786	0.0000	1.0000
SYM	40	-1958.6199	4004.8149	0.0000	1.0000
F81	38	-1963.5186	4009.8509	0.0000	1.0000
K2P	36	-1966.0312	4010.1585	0.0000	1.0000
JC69G	36	-1996.1918	4070.4797	0.0000	1.0000
JC69IG	37	-1996.2028	4072.8551	0.0000	1.0000
JC69I	36	-1997.7660	4073.6282	0.0000	1.0000
JC69	35	-2008.6719	4093.0972	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1893.4798	3874.9596	0.7152	0.7152
GTRIG	45	-1893.4115	3876.8229	0.2817	0.9970
GTRI	44	-1899.6805	3887.3609	0.0015	0.9984
HKYG	40	-1904.2253	3888.4505	0.0008	0.9992
HKYIG	41	-1903.6112	3889.2223	0.0006	0.9998
HKYI	40	-1905.7643	3891.5285	0.0002	1.0000
GTR	43	-1911.4483	3908.8967	0.0000	1.0000
HKY	39	-1917.2647	3912.5294	0.0000	1.0000
SYMG	41	-1941.8835	3965.7669	0.0000	1.0000
K2PG	37	-1950.3538	3974.7077	0.0000	1.0000
SYMIG	42	-1945.6772	3975.3543	0.0000	1.0000
SYMI	41	-1947.0345	3976.0691	0.0000	1.0000
F81G	39	-1949.9346	3977.8692	0.0000	1.0000
K2PIG	38	-1954.2522	3984.5045	0.0000	1.0000
K2PI	37	-1956.1297	3986.2593	0.0000	1.0000
F81IG	40	-1955.7962	3991.5924	0.0000	1.0000
F81I	39	-1957.8448	3993.6896	0.0000	1.0000
SYM	40	-1958.6199	3997.2398	0.0000	1.0000
F81	38	-1963.5186	4003.0371	0.0000	1.0000
K2P	36	-1966.0312	4004.0624	0.0000	1.0000
JC69G	36	-1996.1918	4064.3836	0.0000	1.0000
JC69IG	37	-1996.2028	4066.4056	0.0000	1.0000
JC69I	36	-1997.7660	4067.5321	0.0000	1.0000
JC69	35	-2008.6719	4087.3438	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1904.2253	4054.8988	0.6593	0.6593
HKYI	40	-1905.7643	4057.9768	0.1415	0.8008
GTRG	44	-1893.4798	4058.0527	0.1362	0.9370
HKYIG	41	-1903.6112	4059.8318	0.0560	0.9930
GTRIG	45	-1893.4115	4064.0772	0.0067	0.9997
GTRI	44	-1899.6805	4070.4541	0.0003	1.0000
HKY	39	-1917.2647	4074.8165	0.0000	1.0000
GTR	43	-1911.4483	4087.8286	0.0000	1.0000
K2PG	37	-1950.3538	4128.6723	0.0000	1.0000
SYMG	41	-1941.8835	4136.3764	0.0000	1.0000
F81G	39	-1949.9346	4140.1562	0.0000	1.0000
K2PI	37	-1956.1297	4140.2240	0.0000	1.0000
K2PIG	38	-1954.2522	4142.6303	0.0000	1.0000
SYMI	41	-1947.0345	4146.6786	0.0000	1.0000
SYMIG	42	-1945.6772	4150.1250	0.0000	1.0000
K2P	36	-1966.0312	4153.8659	0.0000	1.0000
F81I	39	-1957.8448	4155.9767	0.0000	1.0000
F81IG	40	-1955.7962	4158.0407	0.0000	1.0000
F81	38	-1963.5186	4161.1630	0.0000	1.0000
SYM	40	-1958.6199	4163.6881	0.0000	1.0000
JC69G	36	-1996.1918	4214.1871	0.0000	1.0000
JC69I	36	-1997.7660	4217.3355	0.0000	1.0000
JC69IG	37	-1996.2028	4220.3703	0.0000	1.0000
JC69	35	-2008.6719	4232.9860	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/chr13_187.phylip = 1 - 474;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_187.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/chr13_187.phylip = 1 - 474;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_187.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/chr13_187.phylip = 1 - 474;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_187.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

