
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:50 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_10260.phylip" (19 taxa, 737 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	-1780.1410	3644.9946	0.4019	0.4019
HKYIG	41	-1779.4098	3645.7750	0.2721	0.6740
HKYI	40	-1780.6393	3645.9912	0.2442	0.9182
GTRG	44	-1778.0530	3649.8285	0.0358	0.9541
GTRIG	45	-1777.2648	3650.5208	0.0254	0.9794
GTRI	44	-1778.6091	3650.9407	0.0206	1.0000
K2PG	37	-1800.0705	3678.1639	0.0000	1.0000
K2PIG	38	-1799.4026	3679.0517	0.0000	1.0000
K2PI	37	-1800.5679	3679.1586	0.0000	1.0000
HKY	39	-1799.1736	3680.8235	0.0000	1.0000
SYMG	41	-1799.2785	3685.5124	0.0000	1.0000
GTR	43	-1797.2440	3685.9483	0.0000	1.0000
SYMI	41	-1799.7382	3686.4318	0.0000	1.0000
SYMIG	42	-1798.6633	3686.5311	0.0000	1.0000
F81G	39	-1809.0506	3700.5775	0.0000	1.0000
F81I	39	-1809.5835	3701.6434	0.0000	1.0000
F81IG	40	-1808.4825	3701.6777	0.0000	1.0000
K2P	36	-1818.4603	3712.7263	0.0000	1.0000
SYM	40	-1817.6075	3719.9277	0.0000	1.0000
JC69G	36	-1826.6560	3729.1176	0.0000	1.0000
JC69I	36	-1827.1876	3730.1808	0.0000	1.0000
JC69IG	37	-1826.1096	3730.2421	0.0000	1.0000
F81	38	-1826.6557	3733.5578	0.0000	1.0000
JC69	35	-1844.0469	3761.6886	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1780.1410	3640.2820	0.3671	0.3671
HKYIG	41	-1779.4098	3640.8196	0.2806	0.6477
HKYI	40	-1780.6393	3641.2785	0.2230	0.8707
GTRG	44	-1778.0530	3644.1060	0.0543	0.9250
GTRIG	45	-1777.2648	3644.5295	0.0439	0.9689
GTRI	44	-1778.6091	3645.2181	0.0311	1.0000
K2PG	37	-1800.0705	3674.1410	0.0000	1.0000
K2PIG	38	-1799.4026	3674.8053	0.0000	1.0000
K2PI	37	-1800.5679	3675.1357	0.0000	1.0000
HKY	39	-1799.1736	3676.3471	0.0000	1.0000
GTR	43	-1797.2440	3680.4880	0.0000	1.0000
SYMG	41	-1799.2785	3680.5570	0.0000	1.0000
SYMIG	42	-1798.6633	3681.3265	0.0000	1.0000
SYMI	41	-1799.7382	3681.4764	0.0000	1.0000
F81G	39	-1809.0506	3696.1011	0.0000	1.0000
F81IG	40	-1808.4825	3696.9651	0.0000	1.0000
F81I	39	-1809.5835	3697.1670	0.0000	1.0000
K2P	36	-1818.4603	3708.9206	0.0000	1.0000
SYM	40	-1817.6075	3715.2151	0.0000	1.0000
JC69G	36	-1826.6560	3725.3119	0.0000	1.0000
JC69IG	37	-1826.1096	3726.2192	0.0000	1.0000
JC69I	36	-1827.1876	3726.3751	0.0000	1.0000
F81	38	-1826.6557	3729.3113	0.0000	1.0000
JC69	35	-1844.0469	3758.0938	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1780.1410	3824.3855	0.5938	0.5938
HKYI	40	-1780.6393	3825.3821	0.3608	0.9545
HKYIG	41	-1779.4098	3829.5257	0.0454	0.9999
K2PG	37	-1800.0705	3844.4368	0.0000	1.0000
K2PI	37	-1800.5679	3845.4315	0.0000	1.0000
GTRG	44	-1778.0530	3846.6199	0.0000	1.0000
GTRI	44	-1778.6091	3847.7320	0.0000	1.0000
K2PIG	38	-1799.4026	3849.7036	0.0000	1.0000
GTRIG	45	-1777.2648	3851.6460	0.0000	1.0000
HKY	39	-1799.1736	3855.8481	0.0000	1.0000
SYMG	41	-1799.2785	3869.2631	0.0000	1.0000
SYMI	41	-1799.7382	3870.1825	0.0000	1.0000
K2P	36	-1818.4603	3874.6138	0.0000	1.0000
SYMIG	42	-1798.6633	3874.6352	0.0000	1.0000
F81G	39	-1809.0506	3875.6021	0.0000	1.0000
F81I	39	-1809.5835	3876.6680	0.0000	1.0000
GTR	43	-1797.2440	3878.3992	0.0000	1.0000
F81IG	40	-1808.4825	3881.0686	0.0000	1.0000
JC69G	36	-1826.6560	3891.0051	0.0000	1.0000
JC69I	36	-1827.1876	3892.0683	0.0000	1.0000
JC69IG	37	-1826.1096	3896.5150	0.0000	1.0000
SYM	40	-1817.6075	3899.3186	0.0000	1.0000
F81	38	-1826.6557	3904.2097	0.0000	1.0000
JC69	35	-1844.0469	3919.1843	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_10260.phylip = 1 - 737;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10260.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_10260.phylip = 1 - 737;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10260.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_10260.phylip = 1 - 737;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10260.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

