
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:35 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/chr5_11656.phylip" (19 taxa, 682 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	-1896.3619	3877.8407	0.5068	0.5068
HKYI	40	-1897.1171	3879.3511	0.2382	0.7450
HKYIG	41	-1896.0866	3879.5545	0.2151	0.9601
GTRG	44	-1894.9872	3884.1911	0.0212	0.9813
GTRI	44	-1895.7289	3885.6744	0.0101	0.9914
GTRIG	45	-1894.7364	3885.9823	0.0086	1.0000
HKY	39	-1913.9700	3910.7998	0.0000	1.0000
K2PG	37	-1917.4072	3913.1808	0.0000	1.0000
K2PI	37	-1917.7908	3913.9480	0.0000	1.0000
K2PIG	38	-1917.0941	3914.7979	0.0000	1.0000
GTR	43	-1912.6216	3917.1741	0.0000	1.0000
SYMG	41	-1916.8429	3921.0670	0.0000	1.0000
F81G	39	-1919.3430	3921.5459	0.0000	1.0000
SYMI	41	-1917.1886	3921.7584	0.0000	1.0000
SYMIG	42	-1916.5374	3922.7273	0.0000	1.0000
F81I	39	-1920.0240	3922.9078	0.0000	1.0000
F81IG	40	-1919.1007	3923.3183	0.0000	1.0000
K2P	36	-1934.8011	3945.7325	0.0000	1.0000
JC69G	36	-1938.1554	3952.4411	0.0000	1.0000
F81	38	-1936.2540	3953.1176	0.0000	1.0000
JC69I	36	-1938.4943	3953.1188	0.0000	1.0000
SYM	40	-1934.2559	3953.6287	0.0000	1.0000
JC69IG	37	-1937.8783	3954.1232	0.0000	1.0000
JC69	35	-1954.8889	3983.6787	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1896.3619	3872.7237	0.4772	0.4772
HKYIG	41	-1896.0866	3874.1732	0.2312	0.7084
HKYI	40	-1897.1171	3874.2341	0.2243	0.9326
GTRG	44	-1894.9872	3877.9744	0.0346	0.9672
GTRI	44	-1895.7289	3879.4578	0.0165	0.9837
GTRIG	45	-1894.7364	3879.4728	0.0163	1.0000
HKY	39	-1913.9700	3905.9400	0.0000	1.0000
K2PG	37	-1917.4072	3908.8143	0.0000	1.0000
K2PI	37	-1917.7908	3909.5816	0.0000	1.0000
K2PIG	38	-1917.0941	3910.1882	0.0000	1.0000
GTR	43	-1912.6216	3911.2431	0.0000	1.0000
SYMG	41	-1916.8429	3915.6857	0.0000	1.0000
SYMI	41	-1917.1886	3916.3772	0.0000	1.0000
F81G	39	-1919.3430	3916.6860	0.0000	1.0000
SYMIG	42	-1916.5374	3917.0747	0.0000	1.0000
F81I	39	-1920.0240	3918.0480	0.0000	1.0000
F81IG	40	-1919.1007	3918.2013	0.0000	1.0000
K2P	36	-1934.8011	3941.6022	0.0000	1.0000
JC69G	36	-1938.1554	3948.3108	0.0000	1.0000
F81	38	-1936.2540	3948.5080	0.0000	1.0000
SYM	40	-1934.2559	3948.5117	0.0000	1.0000
JC69I	36	-1938.4943	3948.9886	0.0000	1.0000
JC69IG	37	-1937.8783	3949.7567	0.0000	1.0000
JC69	35	-1954.8889	3979.7777	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1896.3619	4053.7249	0.6577	0.6577
HKYI	40	-1897.1171	4055.2353	0.3091	0.9668
HKYIG	41	-1896.0866	4059.6994	0.0332	1.0000
K2PG	37	-1917.4072	4076.2404	0.0000	1.0000
K2PI	37	-1917.7908	4077.0077	0.0000	1.0000
GTRG	44	-1894.9872	4077.0757	0.0000	1.0000
GTRI	44	-1895.7289	4078.5591	0.0000	1.0000
K2PIG	38	-1917.0941	4082.1394	0.0000	1.0000
HKY	39	-1913.9700	4082.4161	0.0000	1.0000
GTRIG	45	-1894.7364	4083.0992	0.0000	1.0000
F81G	39	-1919.3430	4093.1622	0.0000	1.0000
F81I	39	-1920.0240	4094.5241	0.0000	1.0000
F81IG	40	-1919.1007	4099.2025	0.0000	1.0000
SYMG	41	-1916.8429	4101.2120	0.0000	1.0000
SYMI	41	-1917.1886	4101.9034	0.0000	1.0000
K2P	36	-1934.8011	4104.5033	0.0000	1.0000
GTR	43	-1912.6216	4105.8194	0.0000	1.0000
SYMIG	42	-1916.5374	4107.1260	0.0000	1.0000
JC69G	36	-1938.1554	4111.2119	0.0000	1.0000
JC69I	36	-1938.4943	4111.8896	0.0000	1.0000
JC69IG	37	-1937.8783	4117.1828	0.0000	1.0000
F81	38	-1936.2540	4120.4591	0.0000	1.0000
SYM	40	-1934.2559	4129.5129	0.0000	1.0000
JC69	35	-1954.8889	4138.1538	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/chr5_11656.phylip = 1 - 682;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11656.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/chr5_11656.phylip = 1 - 682;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11656.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/chr5_11656.phylip = 1 - 682;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11656.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

