
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:54 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/chr2_12867.phylip" (19 taxa, 319 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
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
HKYG	40	-784.4918	1660.7822	0.2916	0.2916
HKYI	40	-784.6677	1661.1340	0.2445	0.5361
HKYIG	41	-783.7248	1661.8828	0.1682	0.7043
GTRG	44	-780.0151	1662.4827	0.1246	0.8289
GTRIG	45	-779.1124	1663.3896	0.0792	0.9080
GTRI	44	-780.5295	1663.5115	0.0745	0.9825
F81G	39	-789.4989	1668.1807	0.0072	0.9897
F81I	39	-789.6493	1668.4814	0.0062	0.9959
F81IG	40	-788.7839	1669.3664	0.0040	0.9999
K2PG	37	-797.7511	1679.5094	0.0000	1.0000
K2PI	37	-797.8418	1679.6908	0.0000	1.0000
K2PIG	38	-796.9491	1680.4838	0.0000	1.0000
HKY	39	-797.8994	1684.9816	0.0000	1.0000
GTR	43	-792.6263	1685.0125	0.0000	1.0000
JC69G	36	-802.0935	1685.6338	0.0000	1.0000
JC69I	36	-802.1940	1685.8349	0.0000	1.0000
SYMG	41	-795.7249	1685.8830	0.0000	1.0000
SYMI	41	-795.9819	1686.3969	0.0000	1.0000
JC69IG	37	-801.3544	1686.7159	0.0000	1.0000
SYMIG	42	-794.8736	1686.8341	0.0000	1.0000
F81	38	-802.8936	1692.3728	0.0000	1.0000
K2P	36	-811.6395	1704.7259	0.0000	1.0000
SYM	40	-808.6827	1709.1639	0.0000	1.0000
JC69	35	-815.8353	1710.5752	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-780.0151	1648.0301	0.2399	0.2399
GTRIG	45	-779.1124	1648.2247	0.2177	0.4576
HKYG	40	-784.4918	1648.9836	0.1489	0.6066
GTRI	44	-780.5295	1649.0590	0.1434	0.7500
HKYI	40	-784.6677	1649.3354	0.1249	0.8749
HKYIG	41	-783.7248	1649.4496	0.1180	0.9929
F81G	39	-789.4989	1656.9979	0.0027	0.9956
F81I	39	-789.6493	1657.2986	0.0023	0.9979
F81IG	40	-788.7839	1657.5678	0.0020	1.0000
K2PG	37	-797.7511	1669.5023	0.0000	1.0000
K2PI	37	-797.8418	1669.6837	0.0000	1.0000
K2PIG	38	-796.9491	1669.8981	0.0000	1.0000
GTR	43	-792.6263	1671.2525	0.0000	1.0000
SYMG	41	-795.7249	1673.4498	0.0000	1.0000
SYMIG	42	-794.8736	1673.7472	0.0000	1.0000
HKY	39	-797.8994	1673.7988	0.0000	1.0000
SYMI	41	-795.9819	1673.9637	0.0000	1.0000
JC69G	36	-802.0935	1676.1870	0.0000	1.0000
JC69I	36	-802.1940	1676.3881	0.0000	1.0000
JC69IG	37	-801.3544	1676.7088	0.0000	1.0000
F81	38	-802.8936	1681.7871	0.0000	1.0000
K2P	36	-811.6395	1695.2791	0.0000	1.0000
SYM	40	-808.6827	1697.3653	0.0000	1.0000
JC69	35	-815.8353	1701.6706	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-784.4918	1799.5913	0.4501	0.4501
HKYI	40	-784.6677	1799.9430	0.3775	0.8276
HKYIG	41	-783.7248	1803.8225	0.0543	0.8819
F81G	39	-789.4989	1803.8403	0.0538	0.9357
F81I	39	-789.6493	1804.1410	0.0463	0.9819
F81IG	40	-788.7839	1808.1754	0.0062	0.9881
K2PG	37	-797.7511	1808.8143	0.0045	0.9926
K2PI	37	-797.8418	1808.9958	0.0041	0.9967
JC69G	36	-802.0935	1811.7339	0.0010	0.9977
JC69I	36	-802.1940	1811.9350	0.0009	0.9986
K2PIG	38	-796.9491	1812.9754	0.0006	0.9992
GTRG	44	-780.0151	1813.6985	0.0004	0.9996
GTRI	44	-780.5295	1814.7274	0.0002	0.9998
JC69IG	37	-801.3544	1816.0209	0.0001	0.9999
GTRIG	45	-779.1124	1817.6583	0.0001	1.0000
HKY	39	-797.8994	1820.6412	0.0000	1.0000
F81	38	-802.8936	1824.8644	0.0000	1.0000
SYMG	41	-795.7249	1827.8226	0.0000	1.0000
SYMI	41	-795.9819	1828.3366	0.0000	1.0000
K2P	36	-811.6395	1830.8260	0.0000	1.0000
SYMIG	42	-794.8736	1831.8852	0.0000	1.0000
GTR	43	-792.6263	1833.1557	0.0000	1.0000
JC69	35	-815.8353	1833.4523	0.0000	1.0000
SYM	40	-808.6827	1847.9730	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/chr2_12867.phylip = 1 - 319;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12867.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12867.phylip = 1 - 319;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12867.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;


[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/chr2_12867.phylip = 1 - 319;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12867.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

