
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:35 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_31749.phylip" (19 taxa, 386 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	-769.8859	1629.2791	0.4002	0.4002
HKYG	40	-769.9467	1629.4006	0.3766	0.7768
HKYIG	41	-770.0266	1632.0647	0.0994	0.8762
HKY	39	-773.2544	1633.5261	0.0479	0.9241
GTRI	44	-767.3077	1634.2283	0.0337	0.9578
GTRG	44	-767.6018	1634.8166	0.0251	0.9829
GTR	43	-769.8302	1636.7247	0.0097	0.9926
GTRIG	45	-767.5385	1637.2534	0.0074	1.0000
K2PI	37	-789.8137	1661.7078	0.0000	1.0000
K2PG	37	-789.8715	1661.8234	0.0000	1.0000
K2PIG	38	-789.9643	1664.4704	0.0000	1.0000
SYMI	41	-786.8280	1665.6676	0.0000	1.0000
SYMG	41	-786.8722	1665.7561	0.0000	1.0000
K2P	36	-793.1076	1665.8485	0.0000	1.0000
SYM	40	-789.2469	1668.0011	0.0000	1.0000
SYMIG	42	-786.8775	1668.2857	0.0000	1.0000
F81G	39	-791.2494	1669.5161	0.0000	1.0000
F81I	39	-791.3139	1669.6452	0.0000	1.0000
F81IG	40	-791.2082	1671.9236	0.0000	1.0000
F81	38	-794.4886	1673.5190	0.0000	1.0000
JC69G	36	-808.8988	1697.4309	0.0000	1.0000
JC69I	36	-808.9710	1697.5753	0.0000	1.0000
JC69IG	37	-808.8607	1699.8019	0.0000	1.0000
JC69	35	-812.0980	1701.3960	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-769.8859	1619.7718	0.3450	0.3450
HKYG	40	-769.9467	1619.8933	0.3247	0.6697
HKYIG	41	-770.0266	1622.0531	0.1103	0.7799
GTRI	44	-767.3077	1622.6154	0.0832	0.8632
GTRG	44	-767.6018	1623.2037	0.0620	0.9252
HKY	39	-773.2544	1624.5087	0.0323	0.9575
GTRIG	45	-767.5385	1625.0769	0.0243	0.9818
GTR	43	-769.8302	1625.6603	0.0182	1.0000
K2PI	37	-789.8137	1653.6274	0.0000	1.0000
K2PG	37	-789.8715	1653.7429	0.0000	1.0000
SYMI	41	-786.8280	1655.6559	0.0000	1.0000
SYMG	41	-786.8722	1655.7445	0.0000	1.0000
K2PIG	38	-789.9643	1655.9286	0.0000	1.0000
SYMIG	42	-786.8775	1657.7550	0.0000	1.0000
K2P	36	-793.1076	1658.2153	0.0000	1.0000
SYM	40	-789.2469	1658.4939	0.0000	1.0000
F81G	39	-791.2494	1660.4988	0.0000	1.0000
F81I	39	-791.3139	1660.6279	0.0000	1.0000
F81IG	40	-791.2082	1662.4164	0.0000	1.0000
F81	38	-794.4886	1664.9772	0.0000	1.0000
JC69G	36	-808.8988	1689.7977	0.0000	1.0000
JC69I	36	-808.9710	1689.9421	0.0000	1.0000
JC69IG	37	-808.8607	1691.7214	0.0000	1.0000
JC69	35	-812.0980	1694.1960	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-769.8859	1778.0053	0.3756	0.3756
HKYG	40	-769.9467	1778.1268	0.3535	0.7291
HKY	39	-773.2544	1778.7864	0.2542	0.9833
HKYIG	41	-770.0266	1784.2424	0.0166	0.9999
GTR	43	-769.8302	1795.7613	0.0001	0.9999
GTRI	44	-767.3077	1796.6723	0.0000	1.0000
GTRG	44	-767.6018	1797.2605	0.0000	1.0000
K2PI	37	-789.8137	1799.9934	0.0000	1.0000
K2PG	37	-789.8715	1800.1089	0.0000	1.0000
K2P	36	-793.1076	1800.6254	0.0000	1.0000
GTRIG	45	-767.5385	1803.0896	0.0000	1.0000
K2PIG	38	-789.9643	1806.2504	0.0000	1.0000
F81G	39	-791.2494	1814.7764	0.0000	1.0000
F81I	39	-791.3139	1814.9056	0.0000	1.0000
F81	38	-794.4886	1815.2990	0.0000	1.0000
SYM	40	-789.2469	1816.7274	0.0000	1.0000
SYMI	41	-786.8280	1817.8453	0.0000	1.0000
SYMG	41	-786.8722	1817.9338	0.0000	1.0000
F81IG	40	-791.2082	1820.6499	0.0000	1.0000
SYMIG	42	-786.8775	1823.9002	0.0000	1.0000
JC69G	36	-808.8988	1832.2078	0.0000	1.0000
JC69I	36	-808.9710	1832.3522	0.0000	1.0000
JC69	35	-812.0980	1832.6503	0.0000	1.0000
JC69IG	37	-808.8607	1838.0874	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_31749.phylip = 1 - 386;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31749.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_31749.phylip = 1 - 386;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31749.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_31749.phylip = 1 - 386;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31749.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

