
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:13 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/chr13_711.phylip" (19 taxa, 303 characters)

Minimum AIC  model: GTRI
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	-841.5689	1775.6569	0.3186	0.3186
HKYG	40	-841.8269	1776.1728	0.2461	0.5647
GTRI	44	-836.9272	1777.2032	0.1470	0.7118
GTRG	44	-837.2236	1777.7961	0.1093	0.8211
HKYIG	41	-841.5762	1778.3478	0.0830	0.9041
HKY	39	-844.7951	1779.4534	0.0477	0.9518
GTRIG	45	-836.9337	1779.9763	0.0368	0.9886
GTR	43	-840.8525	1782.3151	0.0114	1.0000
F81I	39	-852.9482	1795.7595	0.0000	1.0000
F81G	39	-853.1721	1796.2074	0.0000	1.0000
F81IG	40	-852.9543	1798.4277	0.0000	1.0000
F81	38	-855.8801	1798.9875	0.0000	1.0000
K2PI	37	-857.7431	1800.0976	0.0000	1.0000
K2PG	37	-857.9630	1800.5374	0.0000	1.0000
K2PIG	38	-857.7491	1802.7256	0.0000	1.0000
K2P	36	-860.6662	1803.3475	0.0000	1.0000
SYMI	41	-856.4891	1808.1736	0.0000	1.0000
SYMG	41	-856.7308	1808.6570	0.0000	1.0000
SYMIG	42	-856.4956	1810.8835	0.0000	1.0000
SYM	40	-859.4199	1811.3588	0.0000	1.0000
JC69I	36	-866.9482	1815.9114	0.0000	1.0000
JC69G	36	-867.1559	1816.3269	0.0000	1.0000
JC69IG	37	-866.9541	1818.5194	0.0000	1.0000
JC69	35	-869.7900	1819.0183	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-836.9272	1761.8544	0.2990	0.2990
GTRG	44	-837.2236	1762.4472	0.2223	0.5212
HKYI	40	-841.5689	1763.1378	0.1574	0.6786
HKYG	40	-841.8269	1763.6537	0.1216	0.8002
GTRIG	45	-836.9337	1763.8673	0.1093	0.9095
HKYIG	41	-841.5762	1765.1524	0.0575	0.9670
HKY	39	-844.7951	1767.5903	0.0170	0.9839
GTR	43	-840.8525	1767.7050	0.0160	1.0000
F81I	39	-852.9482	1783.8964	0.0000	1.0000
F81G	39	-853.1721	1784.3442	0.0000	1.0000
F81IG	40	-852.9543	1785.9086	0.0000	1.0000
F81	38	-855.8801	1787.7602	0.0000	1.0000
K2PI	37	-857.7431	1789.4862	0.0000	1.0000
K2PG	37	-857.9630	1789.9261	0.0000	1.0000
K2PIG	38	-857.7491	1791.4983	0.0000	1.0000
K2P	36	-860.6662	1793.3324	0.0000	1.0000
SYMI	41	-856.4891	1794.9782	0.0000	1.0000
SYMG	41	-856.7308	1795.4616	0.0000	1.0000
SYMIG	42	-856.4956	1796.9912	0.0000	1.0000
SYM	40	-859.4199	1798.8397	0.0000	1.0000
JC69I	36	-866.9482	1805.8964	0.0000	1.0000
JC69G	36	-867.1559	1806.3119	0.0000	1.0000
JC69IG	37	-866.9541	1807.9081	0.0000	1.0000
JC69	35	-869.7900	1809.5801	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-841.5689	1911.6871	0.3960	0.3960
HKYG	40	-841.8269	1912.2031	0.3060	0.7020
HKY	39	-844.7951	1912.4258	0.2737	0.9757
HKYIG	41	-841.5762	1917.4155	0.0226	0.9983
GTRI	44	-836.9272	1925.2586	0.0004	0.9987
GTRG	44	-837.2236	1925.8515	0.0003	0.9990
K2PI	37	-857.7431	1926.8944	0.0002	0.9992
K2P	36	-860.6662	1927.0268	0.0002	0.9994
K2PG	37	-857.9630	1927.3342	0.0002	0.9996
GTR	43	-840.8525	1927.3955	0.0002	0.9997
F81I	39	-852.9482	1928.7320	0.0001	0.9998
F81	38	-855.8801	1928.8821	0.0001	0.9999
F81G	39	-853.1721	1929.1798	0.0001	1.0000
GTRIG	45	-836.9337	1930.9853	0.0000	1.0000
K2PIG	38	-857.7491	1932.6201	0.0000	1.0000
F81IG	40	-852.9543	1934.4579	0.0000	1.0000
JC69	35	-869.7900	1939.5607	0.0000	1.0000
JC69I	36	-866.9482	1939.5908	0.0000	1.0000
JC69G	36	-867.1559	1940.0062	0.0000	1.0000
JC69IG	37	-866.9541	1945.3162	0.0000	1.0000
SYMI	41	-856.4891	1947.2413	0.0000	1.0000
SYM	40	-859.4199	1947.3891	0.0000	1.0000
SYMG	41	-856.7308	1947.7246	0.0000	1.0000
SYMIG	42	-856.4956	1952.9680	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/chr13_711.phylip = 1 - 303;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_711.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/chr13_711.phylip = 1 - 303;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_711.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/chr13_711.phylip = 1 - 303;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_711.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

