
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:09 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_4732.phylip" (19 taxa, 325 characters)

Minimum AIC  model: HKYI
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	-838.7077	1768.9648	0.2979	0.2979
HKYG	40	-838.7530	1769.0553	0.2847	0.5825
HKYIG	41	-838.3339	1770.8375	0.1168	0.6993
GTRI	44	-835.0996	1772.3421	0.0550	0.7543
GTRG	44	-835.1033	1772.3495	0.0548	0.8092
K2PI	37	-844.4093	1772.6164	0.0480	0.8571
K2PG	37	-844.4623	1772.7226	0.0455	0.9026
F81G	39	-842.3084	1773.5642	0.0299	0.9325
GTRIG	45	-834.6619	1774.1626	0.0221	0.9546
K2PIG	38	-844.0550	1774.4737	0.0190	0.9736
SYMI	41	-840.9433	1776.0563	0.0086	0.9822
SYMG	41	-840.9693	1776.1083	0.0084	0.9906
JC69G	36	-848.0540	1777.3580	0.0045	0.9951
SYMIG	42	-840.6049	1778.0182	0.0032	0.9983
F81I	39	-845.6336	1780.2146	0.0011	0.9993
F81IG	40	-845.2354	1782.0200	0.0004	0.9998
JC69I	36	-851.4156	1784.0812	0.0002	0.9999
JC69IG	37	-851.0598	1785.9175	0.0001	1.0000
HKY	39	-856.4925	1801.9324	0.0000	1.0000
GTR	43	-852.6234	1804.7129	0.0000	1.0000
K2P	36	-862.2838	1805.8176	0.0000	1.0000
SYM	40	-858.5960	1808.7412	0.0000	1.0000
F81	38	-863.2301	1812.8237	0.0000	1.0000
JC69	35	-869.0824	1816.8846	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-838.7077	1757.4155	0.2187	0.2187
HKYG	40	-838.7530	1757.5060	0.2090	0.4278
GTRI	44	-835.0996	1758.1992	0.1478	0.5756
GTRG	44	-835.1033	1758.2066	0.1473	0.7229
HKYIG	41	-838.3339	1758.6679	0.1169	0.8398
GTRIG	45	-834.6619	1759.3239	0.0842	0.9240
F81G	39	-842.3084	1762.6169	0.0162	0.9403
K2PI	37	-844.4093	1762.8185	0.0147	0.9550
K2PG	37	-844.4623	1762.9247	0.0139	0.9689
SYMI	41	-840.9433	1763.8867	0.0086	0.9775
SYMG	41	-840.9693	1763.9387	0.0084	0.9859
K2PIG	38	-844.0550	1764.1101	0.0077	0.9936
SYMIG	42	-840.6049	1765.2097	0.0044	0.9980
JC69G	36	-848.0540	1768.1080	0.0010	0.9990
F81I	39	-845.6336	1769.2673	0.0006	0.9996
F81IG	40	-845.2354	1770.4707	0.0003	0.9999
JC69I	36	-851.4156	1774.8312	0.0000	1.0000
JC69IG	37	-851.0598	1776.1196	0.0000	1.0000
HKY	39	-856.4925	1790.9851	0.0000	1.0000
GTR	43	-852.6234	1791.2467	0.0000	1.0000
K2P	36	-862.2838	1796.5676	0.0000	1.0000
SYM	40	-858.5960	1797.1919	0.0000	1.0000
F81	38	-863.2301	1802.4601	0.0000	1.0000
JC69	35	-869.0824	1808.1649	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-844.4093	1902.8201	0.3778	0.3778
K2PG	37	-844.4623	1902.9262	0.3583	0.7361
JC69G	36	-848.0540	1904.3257	0.1780	0.9141
K2PIG	38	-844.0550	1907.8954	0.0299	0.9439
HKYI	40	-838.7077	1908.7685	0.0193	0.9632
HKYG	40	-838.7530	1908.8590	0.0184	0.9817
F81G	39	-842.3084	1910.1860	0.0095	0.9912
JC69I	36	-851.4156	1911.0489	0.0062	0.9973
HKYIG	41	-838.3339	1913.8047	0.0016	0.9989
JC69IG	37	-851.0598	1916.1211	0.0005	0.9994
F81I	39	-845.6336	1916.8364	0.0003	0.9997
SYMI	41	-840.9433	1919.0235	0.0001	0.9998
SYMG	41	-840.9693	1919.0755	0.0001	0.9999
F81IG	40	-845.2354	1921.8237	0.0000	1.0000
SYMIG	42	-840.6049	1924.1304	0.0000	1.0000
GTRI	44	-835.0996	1924.6875	0.0000	1.0000
GTRG	44	-835.1033	1924.6949	0.0000	1.0000
GTRIG	45	-834.6619	1929.5960	0.0000	1.0000
K2P	36	-862.2838	1932.7853	0.0000	1.0000
HKY	39	-856.4925	1938.5542	0.0000	1.0000
JC69	35	-869.0824	1940.5988	0.0000	1.0000
F81	38	-863.2301	1946.2455	0.0000	1.0000
SYM	40	-858.5960	1948.5449	0.0000	1.0000
GTR	43	-852.6234	1953.9512	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/chr7_4732.phylip = 1 - 325;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4732.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/chr7_4732.phylip = 1 - 325;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4732.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_4732.phylip = 1 - 325;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4732.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;


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End of Output

