
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:06 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/chr2_8593.phylip" (19 taxa, 239 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: HKY


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	-788.7837	1685.9798	0.9738	0.9738
HKY	39	-801.1894	1696.0571	0.0063	0.9801
GTR	43	-795.5204	1696.4459	0.0052	0.9853
HKYG	40	-800.0757	1696.7170	0.0045	0.9899
HKYI	40	-800.1546	1696.8748	0.0042	0.9940
GTRI	44	-794.2716	1696.9555	0.0040	0.9981
HKYIG	41	-800.0784	1699.6390	0.0011	0.9991
GTRIG	45	-794.2820	1700.0148	0.0009	1.0000
K2P	36	-814.7532	1714.6946	0.0000	1.0000
K2PG	37	-813.4682	1714.9265	0.0000	1.0000
K2PI	37	-814.0054	1716.0008	0.0000	1.0000
K2PIG	38	-813.4631	1717.7463	0.0000	1.0000
SYM	40	-811.1859	1718.9374	0.0000	1.0000
SYMI	41	-811.2974	1722.0770	0.0000	1.0000
SYMG	41	-811.4339	1722.3501	0.0000	1.0000
SYMIG	42	-811.4229	1725.2744	0.0000	1.0000
F81G	39	-825.7500	1745.1783	0.0000	1.0000
F81I	39	-830.2425	1754.1633	0.0000	1.0000
F81	38	-832.3470	1755.5141	0.0000	1.0000
F81IG	40	-829.8978	1756.3612	0.0000	1.0000
JC69G	36	-836.3536	1757.8953	0.0000	1.0000
JC69I	36	-840.2378	1765.6638	0.0000	1.0000
JC69IG	37	-839.6957	1767.3814	0.0000	1.0000
JC69	35	-843.0656	1768.5451	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-788.7837	1665.5674	0.9891	0.9891
GTRI	44	-794.2716	1676.5432	0.0041	0.9932
GTR	43	-795.5204	1677.0408	0.0032	0.9964
GTRIG	45	-794.2820	1678.5640	0.0015	0.9979
HKYG	40	-800.0757	1680.1514	0.0007	0.9985
HKYI	40	-800.1546	1680.3092	0.0006	0.9992
HKY	39	-801.1894	1680.3787	0.0006	0.9998
HKYIG	41	-800.0784	1682.1567	0.0002	1.0000
K2PG	37	-813.4682	1700.9364	0.0000	1.0000
K2P	36	-814.7532	1701.5064	0.0000	1.0000
K2PI	37	-814.0054	1702.0107	0.0000	1.0000
SYM	40	-811.1859	1702.3717	0.0000	1.0000
K2PIG	38	-813.4631	1702.9263	0.0000	1.0000
SYMI	41	-811.2974	1704.5948	0.0000	1.0000
SYMG	41	-811.4339	1704.8678	0.0000	1.0000
SYMIG	42	-811.4229	1706.8458	0.0000	1.0000
F81G	39	-825.7500	1729.4999	0.0000	1.0000
F81I	39	-830.2425	1738.4849	0.0000	1.0000
F81IG	40	-829.8978	1739.7956	0.0000	1.0000
F81	38	-832.3470	1740.6941	0.0000	1.0000
JC69G	36	-836.3536	1744.7072	0.0000	1.0000
JC69I	36	-840.2378	1752.4757	0.0000	1.0000
JC69IG	37	-839.6957	1753.3914	0.0000	1.0000
JC69	35	-843.0656	1756.1313	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKY	39	-801.1894	1815.9608	0.5948	0.5948
GTRG	44	-788.7837	1818.5318	0.1645	0.7593
HKYG	40	-800.0757	1819.2099	0.1172	0.8765
HKYI	40	-800.1546	1819.3677	0.1083	0.9848
HKYIG	41	-800.0784	1824.6917	0.0076	0.9923
GTR	43	-795.5204	1826.5287	0.0030	0.9954
K2P	36	-814.7532	1826.6591	0.0028	0.9982
GTRI	44	-794.2716	1829.5076	0.0007	0.9989
K2PG	37	-813.4682	1829.5656	0.0007	0.9995
K2PI	37	-814.0054	1830.6399	0.0004	0.9999
GTRIG	45	-794.2820	1835.0048	0.0000	1.0000
K2PIG	38	-813.4631	1835.0319	0.0000	1.0000
SYM	40	-811.1859	1841.4303	0.0000	1.0000
SYMI	41	-811.2974	1847.1298	0.0000	1.0000
SYMG	41	-811.4339	1847.4028	0.0000	1.0000
SYMIG	42	-811.4229	1852.8573	0.0000	1.0000
F81G	39	-825.7500	1865.0820	0.0000	1.0000
JC69G	36	-836.3536	1869.8599	0.0000	1.0000
F81	38	-832.3470	1872.7997	0.0000	1.0000
F81I	39	-830.2425	1874.0670	0.0000	1.0000
JC69I	36	-840.2378	1877.6284	0.0000	1.0000
JC69	35	-843.0656	1877.8075	0.0000	1.0000
F81IG	40	-829.8978	1878.8541	0.0000	1.0000
JC69IG	37	-839.6957	1882.0205	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_8593.phylip = 1 - 239;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8593.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/chr2_8593.phylip = 1 - 239;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8593.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 (HKY)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8593.phylip = 1 - 239;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8593.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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End of Output

