
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:28 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/chr5_17310.phylip" (19 taxa, 348 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: HKYG


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	-846.6337	1794.3367	0.3571	0.3571
GTRI	44	-847.2544	1795.5782	0.1920	0.5491
GTRIG	45	-845.9437	1795.5959	0.1903	0.7394
HKYG	40	-852.8867	1796.4574	0.1237	0.8631
HKYI	40	-853.3792	1797.4424	0.0756	0.9387
HKYIG	41	-852.3027	1797.8602	0.0613	1.0000
GTR	43	-858.7997	1816.0468	0.0000	1.0000
HKY	39	-864.4287	1816.9873	0.0000	1.0000
K2PG	37	-872.1474	1827.3658	0.0000	1.0000
K2PI	37	-872.5104	1828.0918	0.0000	1.0000
K2PIG	38	-871.5789	1828.7500	0.0000	1.0000
SYMG	41	-869.7253	1832.7054	0.0000	1.0000
SYMI	41	-870.3046	1833.8641	0.0000	1.0000
SYMIG	42	-869.0389	1833.9203	0.0000	1.0000
F81G	39	-875.8592	1839.8483	0.0000	1.0000
F81I	39	-876.2614	1840.6526	0.0000	1.0000
F81IG	40	-875.4172	1841.5185	0.0000	1.0000
K2P	36	-883.8659	1848.2976	0.0000	1.0000
SYM	40	-880.1253	1850.9345	0.0000	1.0000
F81	38	-886.2091	1858.0104	0.0000	1.0000
JC69G	36	-892.0266	1864.6191	0.0000	1.0000
JC69I	36	-892.5088	1865.5835	0.0000	1.0000
JC69IG	37	-891.5643	1866.1996	0.0000	1.0000
JC69	35	-901.4918	1881.0605	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-846.6337	1781.2674	0.3985	0.3985
GTRIG	45	-845.9437	1781.8873	0.2923	0.6907
GTRI	44	-847.2544	1782.5089	0.2142	0.9049
HKYG	40	-852.8867	1785.7733	0.0419	0.9468
HKYIG	41	-852.3027	1786.6053	0.0276	0.9744
HKYI	40	-853.3792	1786.7583	0.0256	1.0000
GTR	43	-858.7997	1803.5994	0.0000	1.0000
HKY	39	-864.4287	1806.8574	0.0000	1.0000
K2PG	37	-872.1474	1818.2948	0.0000	1.0000
K2PI	37	-872.5104	1819.0208	0.0000	1.0000
K2PIG	38	-871.5789	1819.1578	0.0000	1.0000
SYMG	41	-869.7253	1821.4505	0.0000	1.0000
SYMIG	42	-869.0389	1822.0777	0.0000	1.0000
SYMI	41	-870.3046	1822.6092	0.0000	1.0000
F81G	39	-875.8592	1829.7184	0.0000	1.0000
F81I	39	-876.2614	1830.5227	0.0000	1.0000
F81IG	40	-875.4172	1830.8345	0.0000	1.0000
K2P	36	-883.8659	1839.7317	0.0000	1.0000
SYM	40	-880.1253	1840.2505	0.0000	1.0000
F81	38	-886.2091	1848.4182	0.0000	1.0000
JC69G	36	-892.0266	1856.0532	0.0000	1.0000
JC69I	36	-892.5088	1857.0176	0.0000	1.0000
JC69IG	37	-891.5643	1857.1286	0.0000	1.0000
JC69	35	-901.4918	1872.9836	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-852.8867	1939.8614	0.5833	0.5833
HKYI	40	-853.3792	1940.8464	0.3564	0.9397
HKYIG	41	-852.3027	1944.5456	0.0561	0.9958
GTRG	44	-846.6337	1950.7643	0.0025	0.9983
GTRI	44	-847.2544	1952.0058	0.0013	0.9996
GTRIG	45	-845.9437	1955.2364	0.0003	0.9999
HKY	39	-864.4287	1957.0933	0.0001	1.0000
K2PG	37	-872.1474	1960.8263	0.0000	1.0000
K2PI	37	-872.5104	1961.5523	0.0000	1.0000
K2PIG	38	-871.5789	1965.5415	0.0000	1.0000
GTR	43	-858.7997	1969.2441	0.0000	1.0000
K2P	36	-883.8659	1978.4110	0.0000	1.0000
SYMG	41	-869.7253	1979.3908	0.0000	1.0000
F81G	39	-875.8592	1979.9543	0.0000	1.0000
SYMI	41	-870.3046	1980.5495	0.0000	1.0000
F81I	39	-876.2614	1980.7586	0.0000	1.0000
SYMIG	42	-869.0389	1983.8702	0.0000	1.0000
F81IG	40	-875.4172	1984.9226	0.0000	1.0000
SYM	40	-880.1253	1994.3386	0.0000	1.0000
JC69G	36	-892.0266	1994.7325	0.0000	1.0000
F81	38	-886.2091	1994.8019	0.0000	1.0000
JC69I	36	-892.5088	1995.6968	0.0000	1.0000
JC69IG	37	-891.5643	1999.6601	0.0000	1.0000
JC69	35	-901.4918	2007.8106	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/chr5_17310.phylip = 1 - 348;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_17310.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/chr5_17310.phylip = 1 - 348;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_17310.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_17310.phylip = 1 - 348;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_17310.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

