
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:10 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/chr1_32301.phylip" (19 taxa, 309 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: HKYI


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
HKYI	40	-824.7540	1741.7468	0.4560	0.4560
HKYG	40	-824.8283	1741.8954	0.4234	0.8794
HKYIG	41	-824.8456	1744.5902	0.1100	0.9894
GTRI	44	-823.9286	1750.8572	0.0048	0.9942
GTRG	44	-824.0414	1751.0829	0.0043	0.9985
GTRIG	45	-824.0413	1753.8241	0.0011	0.9996
HKY	39	-833.1528	1755.9042	0.0004	1.0000
GTR	43	-832.5051	1765.2895	0.0000	1.0000
F81I	39	-847.7803	1785.1591	0.0000	1.0000
F81G	39	-847.7874	1785.1734	0.0000	1.0000
F81IG	40	-847.7925	1787.8237	0.0000	1.0000
K2PI	37	-855.5370	1795.4505	0.0000	1.0000
K2PG	37	-855.5471	1795.4705	0.0000	1.0000
F81	38	-855.4719	1797.9216	0.0000	1.0000
K2PIG	38	-855.5661	1798.1100	0.0000	1.0000
SYMI	41	-854.1699	1803.2386	0.0000	1.0000
SYMG	41	-855.0160	1804.9310	0.0000	1.0000
SYMIG	42	-855.0111	1807.6012	0.0000	1.0000
K2P	36	-865.4600	1812.7141	0.0000	1.0000
SYM	40	-864.2880	1820.8148	0.0000	1.0000
JC69G	36	-874.8248	1831.4437	0.0000	1.0000
JC69I	36	-874.8694	1831.5328	0.0000	1.0000
JC69IG	37	-874.7954	1833.9672	0.0000	1.0000
JC69	35	-883.3178	1845.8664	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-824.7540	1729.5080	0.4242	0.4242
HKYG	40	-824.8283	1729.6566	0.3938	0.8179
HKYIG	41	-824.8456	1731.6913	0.1424	0.9603
GTRI	44	-823.9286	1735.8572	0.0177	0.9781
GTRG	44	-824.0414	1736.0829	0.0158	0.9939
GTRIG	45	-824.0413	1738.0827	0.0058	0.9997
HKY	39	-833.1528	1744.3057	0.0003	1.0000
GTR	43	-832.5051	1751.0102	0.0000	1.0000
F81I	39	-847.7803	1773.5606	0.0000	1.0000
F81G	39	-847.7874	1773.5748	0.0000	1.0000
F81IG	40	-847.7925	1775.5849	0.0000	1.0000
K2PI	37	-855.5370	1785.0741	0.0000	1.0000
K2PG	37	-855.5471	1785.0941	0.0000	1.0000
F81	38	-855.4719	1786.9439	0.0000	1.0000
K2PIG	38	-855.5661	1787.1322	0.0000	1.0000
SYMI	41	-854.1699	1790.3397	0.0000	1.0000
SYMG	41	-855.0160	1792.0321	0.0000	1.0000
SYMIG	42	-855.0111	1794.0223	0.0000	1.0000
K2P	36	-865.4600	1802.9200	0.0000	1.0000
SYM	40	-864.2880	1808.5760	0.0000	1.0000
JC69G	36	-874.8248	1821.6496	0.0000	1.0000
JC69I	36	-874.8694	1821.7387	0.0000	1.0000
JC69IG	37	-874.7954	1823.5908	0.0000	1.0000
JC69	35	-883.3178	1836.6356	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-824.7540	1878.8417	0.5040	0.5040
HKYG	40	-824.8283	1878.9903	0.4679	0.9718
HKYIG	41	-824.8456	1884.7583	0.0262	0.9980
HKY	39	-833.1528	1889.9060	0.0020	1.0000
GTRI	44	-823.9286	1900.1243	0.0000	1.0000
GTRG	44	-824.0414	1900.3499	0.0000	1.0000
GTRIG	45	-824.0413	1906.0830	0.0000	1.0000
GTR	43	-832.5051	1911.5439	0.0000	1.0000
F81I	39	-847.7803	1919.1609	0.0000	1.0000
F81G	39	-847.7874	1919.1751	0.0000	1.0000
K2PI	37	-855.5370	1923.2077	0.0000	1.0000
K2PG	37	-855.5471	1923.2278	0.0000	1.0000
F81IG	40	-847.7925	1924.9186	0.0000	1.0000
F81	38	-855.4719	1928.8108	0.0000	1.0000
K2PIG	38	-855.5661	1928.9991	0.0000	1.0000
K2P	36	-865.4600	1937.3203	0.0000	1.0000
SYMI	41	-854.1699	1943.4067	0.0000	1.0000
SYMG	41	-855.0160	1945.0991	0.0000	1.0000
SYMIG	42	-855.0111	1950.8226	0.0000	1.0000
JC69G	36	-874.8248	1956.0498	0.0000	1.0000
JC69I	36	-874.8694	1956.1390	0.0000	1.0000
SYM	40	-864.2880	1957.9097	0.0000	1.0000
JC69IG	37	-874.7954	1961.7244	0.0000	1.0000
JC69	35	-883.3178	1967.3026	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32301.phylip = 1 - 309;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32301.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32301.phylip = 1 - 309;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32301.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32301.phylip = 1 - 309;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32301.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

