
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:07 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_5512.phylip" (19 taxa, 212 characters)

Minimum AIC  model: GTRG
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	-746.9467	1593.0747	0.3117	0.3117
HKYI	40	-746.9685	1593.1182	0.3049	0.6166
GTRG	44	-741.6150	1594.9425	0.1225	0.7391
GTRI	44	-741.8813	1595.4753	0.0938	0.8329
HKYIG	41	-746.9460	1596.1508	0.0669	0.8999
HKY	39	-750.2174	1596.5743	0.0542	0.9540
GTRIG	45	-741.6200	1598.1797	0.0243	0.9783
GTR	43	-745.4964	1599.5166	0.0124	0.9908
K2PI	37	-755.7831	1601.7272	0.0041	0.9949
K2PG	37	-755.9802	1602.1213	0.0034	0.9983
K2PIG	38	-755.7878	1604.7086	0.0009	0.9992
K2P	36	-759.7036	1606.6301	0.0004	0.9995
SYMI	41	-752.6821	1607.6230	0.0002	0.9998
SYMG	41	-752.8572	1607.9732	0.0002	0.9999
SYMIG	42	-752.6843	1610.7414	0.0000	1.0000
SYM	40	-756.8425	1612.8662	0.0000	1.0000
F81I	39	-767.0152	1630.1700	0.0000	1.0000
F81G	39	-767.2282	1630.5959	0.0000	1.0000
F81IG	40	-767.0194	1633.2200	0.0000	1.0000
F81	38	-770.3157	1633.7643	0.0000	1.0000
JC69I	36	-774.8084	1636.8397	0.0000	1.0000
JC69G	36	-775.1247	1637.4722	0.0000	1.0000
JC69IG	37	-774.8155	1639.7920	0.0000	1.0000
JC69	35	-778.4078	1641.1338	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-741.6150	1571.2299	0.3524	0.3524
GTRI	44	-741.8813	1571.7627	0.2700	0.6224
GTRIG	45	-741.6200	1573.2399	0.1290	0.7514
HKYG	40	-746.9467	1573.8935	0.0930	0.8445
HKYI	40	-746.9685	1573.9370	0.0910	0.9355
HKYIG	41	-746.9460	1575.8920	0.0343	0.9698
GTR	43	-745.4964	1576.9928	0.0198	0.9895
HKY	39	-750.2174	1578.4348	0.0096	0.9991
K2PI	37	-755.7831	1585.5663	0.0003	0.9994
K2PG	37	-755.9802	1585.9604	0.0002	0.9996
SYMI	41	-752.6821	1587.3642	0.0001	0.9997
K2PIG	38	-755.7878	1587.5757	0.0001	0.9998
SYMG	41	-752.8572	1587.7144	0.0001	0.9999
SYMIG	42	-752.6843	1589.3686	0.0000	1.0000
K2P	36	-759.7036	1591.4073	0.0000	1.0000
SYM	40	-756.8425	1593.6850	0.0000	1.0000
F81I	39	-767.0152	1612.0305	0.0000	1.0000
F81G	39	-767.2282	1612.4564	0.0000	1.0000
F81IG	40	-767.0194	1614.0388	0.0000	1.0000
F81	38	-770.3157	1616.6313	0.0000	1.0000
JC69I	36	-774.8084	1621.6168	0.0000	1.0000
JC69G	36	-775.1247	1622.2493	0.0000	1.0000
JC69IG	37	-774.8155	1623.6311	0.0000	1.0000
JC69	35	-778.4078	1626.8157	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-746.9467	1708.1569	0.2787	0.2787
HKYI	40	-746.9685	1708.2004	0.2727	0.5515
HKY	39	-750.2174	1709.3417	0.1541	0.7056
K2PI	37	-755.7831	1709.7600	0.1250	0.8306
K2PG	37	-755.9802	1710.1541	0.1027	0.9333
K2P	36	-759.7036	1712.2444	0.0361	0.9694
HKYIG	41	-746.9460	1713.5120	0.0192	0.9886
K2PIG	38	-755.7878	1715.1259	0.0085	0.9971
GTRG	44	-741.6150	1718.9197	0.0013	0.9984
GTRI	44	-741.8813	1719.4525	0.0010	0.9994
GTR	43	-745.4964	1721.3260	0.0004	0.9998
GTRIG	45	-741.6200	1724.2863	0.0001	0.9999
SYMI	41	-752.6821	1724.9842	0.0001	0.9999
SYMG	41	-752.8572	1725.3345	0.0001	1.0000
SYM	40	-756.8425	1727.9484	0.0000	1.0000
SYMIG	42	-752.6843	1730.3452	0.0000	1.0000
JC69I	36	-774.8084	1742.4539	0.0000	1.0000
F81I	39	-767.0152	1742.9373	0.0000	1.0000
JC69G	36	-775.1247	1743.0864	0.0000	1.0000
F81G	39	-767.2282	1743.3633	0.0000	1.0000
F81	38	-770.3157	1744.1816	0.0000	1.0000
JC69	35	-778.4078	1744.2962	0.0000	1.0000
JC69IG	37	-774.8155	1747.8248	0.0000	1.0000
F81IG	40	-767.0194	1748.3022	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_5512.phylip = 1 - 212;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5512.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5512.phylip = 1 - 212;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5512.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/chr2_5512.phylip = 1 - 212;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5512.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

