
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:45 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/chr7_6190.phylip" (19 taxa, 281 characters)

Minimum AIC  model: GTRI
Minimum AICc model: HKYI
Minimum BIC  model: K2PI


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	-876.0824	1845.8314	0.3941	0.3941
HKYG	40	-876.3504	1846.3675	0.3014	0.6955
HKYIG	41	-876.0725	1848.5549	0.1010	0.7964
GTRI	44	-871.9221	1848.6238	0.0975	0.8940
GTRG	44	-872.4803	1849.7403	0.0558	0.9498
GTRIG	45	-872.1008	1851.8186	0.0197	0.9695
K2PI	37	-883.5577	1852.6874	0.0128	0.9823
K2PG	37	-883.7753	1853.1226	0.0103	0.9926
K2PIG	38	-883.5368	1855.3215	0.0034	0.9960
SYMI	41	-880.1478	1856.7057	0.0017	0.9977
SYMG	41	-880.4557	1857.3215	0.0013	0.9990
SYMIG	42	-880.1417	1859.4598	0.0004	0.9994
HKY	39	-884.2832	1859.5125	0.0004	0.9999
GTR	43	-879.9324	1861.8310	0.0001	1.0000
K2P	36	-892.0322	1866.9824	0.0000	1.0000
SYM	40	-887.8366	1869.3400	0.0000	1.0000
F81I	39	-899.7992	1890.5444	0.0000	1.0000
F81G	39	-900.0650	1891.0761	0.0000	1.0000
F81IG	40	-899.7956	1893.2579	0.0000	1.0000
JC69I	36	-905.7723	1894.4627	0.0000	1.0000
JC69G	36	-906.0293	1894.9766	0.0000	1.0000
JC69IG	37	-905.7679	1897.1079	0.0000	1.0000
F81	38	-904.9902	1898.2283	0.0000	1.0000
JC69	35	-914.1949	1908.6756	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-871.9221	1831.8442	0.2678	0.2678
HKYI	40	-876.0824	1832.1647	0.2282	0.4960
HKYG	40	-876.3504	1832.7008	0.1745	0.6705
GTRG	44	-872.4803	1832.9607	0.1532	0.8237
HKYIG	41	-876.0725	1834.1449	0.0848	0.9085
GTRIG	45	-872.1008	1834.2016	0.0824	0.9909
K2PI	37	-883.5577	1841.1154	0.0026	0.9935
K2PG	37	-883.7753	1841.5506	0.0021	0.9956
SYMI	41	-880.1478	1842.2957	0.0014	0.9970
SYMG	41	-880.4557	1842.9114	0.0011	0.9981
K2PIG	38	-883.5368	1843.0736	0.0010	0.9991
SYMIG	42	-880.1417	1844.2834	0.0005	0.9996
GTR	43	-879.9324	1845.8648	0.0002	0.9998
HKY	39	-884.2832	1846.5665	0.0002	1.0000
SYM	40	-887.8366	1855.6733	0.0000	1.0000
K2P	36	-892.0322	1856.0644	0.0000	1.0000
F81I	39	-899.7992	1877.5983	0.0000	1.0000
F81G	39	-900.0650	1878.1300	0.0000	1.0000
F81IG	40	-899.7956	1879.5912	0.0000	1.0000
JC69I	36	-905.7723	1883.5446	0.0000	1.0000
JC69G	36	-906.0293	1884.0586	0.0000	1.0000
JC69IG	37	-905.7679	1885.5359	0.0000	1.0000
F81	38	-904.9902	1885.9804	0.0000	1.0000
JC69	35	-914.1949	1898.3899	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-883.5577	1975.7345	0.3914	0.3914
K2PG	37	-883.7753	1976.1697	0.3148	0.7062
HKYI	40	-876.0824	1977.6989	0.1466	0.8527
HKYG	40	-876.3504	1978.2350	0.1121	0.9648
K2PIG	38	-883.5368	1981.3311	0.0238	0.9887
HKYIG	41	-876.0725	1983.3174	0.0088	0.9975
K2P	36	-892.0322	1987.0451	0.0014	0.9989
HKY	39	-884.2832	1988.4623	0.0007	0.9995
SYMI	41	-880.1478	1991.4682	0.0001	0.9997
GTRI	44	-871.9221	1991.9318	0.0001	0.9998
SYMG	41	-880.4557	1992.0840	0.0001	0.9999
GTRG	44	-872.4803	1993.0483	0.0001	1.0000
SYMIG	42	-880.1417	1997.0943	0.0000	1.0000
GTRIG	45	-872.1008	1997.9276	0.0000	1.0000
SYM	40	-887.8366	2001.2075	0.0000	1.0000
GTR	43	-879.9324	2002.3140	0.0000	1.0000
JC69I	36	-905.7723	2014.5254	0.0000	1.0000
JC69G	36	-906.0293	2015.0393	0.0000	1.0000
F81I	39	-899.7992	2019.4941	0.0000	1.0000
F81G	39	-900.0650	2020.0259	0.0000	1.0000
JC69IG	37	-905.7679	2020.1550	0.0000	1.0000
F81	38	-904.9902	2024.2378	0.0000	1.0000
F81IG	40	-899.7956	2025.1254	0.0000	1.0000
JC69	35	-914.1949	2025.7323	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6190.phylip = 1 - 281;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6190.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) 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/chr7_6190.phylip = 1 - 281;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6190.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 (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6190.phylip = 1 - 281;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6190.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


-------------------------------------------------------------
End of Output

