
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:23 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/chr3_13404.phylip" (19 taxa, 319 characters)

Minimum AIC  model: HKYG
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	-794.7701	1681.3387	0.3659	0.3659
HKYIG	41	-793.7891	1682.0114	0.2614	0.6273
HKYI	40	-795.3797	1682.5580	0.1989	0.8261
GTRG	44	-790.9308	1684.3142	0.0826	0.9088
GTRIG	45	-790.0878	1685.3404	0.0495	0.9582
GTRI	44	-791.7213	1685.8951	0.0375	0.9957
K2PG	37	-804.0395	1692.0861	0.0017	0.9974
K2PIG	38	-802.9564	1692.4985	0.0014	0.9988
K2PI	37	-804.5461	1693.0994	0.0010	0.9998
SYMG	41	-802.2740	1698.9813	0.0001	0.9999
SYMIG	42	-801.2433	1699.5735	0.0000	0.9999
SYMI	41	-802.8868	1700.2067	0.0000	1.0000
HKY	39	-806.2467	1701.6762	0.0000	1.0000
F81G	39	-806.3302	1701.8431	0.0000	1.0000
F81IG	40	-805.4105	1702.6196	0.0000	1.0000
F81I	39	-806.9129	1703.0085	0.0000	1.0000
GTR	43	-801.9251	1703.6103	0.0000	1.0000
JC69G	36	-815.8678	1713.1823	0.0000	1.0000
K2P	36	-816.0418	1713.5304	0.0000	1.0000
JC69IG	37	-814.8968	1713.8007	0.0000	1.0000
JC69I	36	-816.4118	1714.2705	0.0000	1.0000
SYM	40	-813.8063	1719.4111	0.0000	1.0000
F81	38	-817.6852	1721.9560	0.0000	1.0000
JC69	35	-827.4738	1733.8521	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-794.7701	1669.5402	0.2224	0.2224
HKYIG	41	-793.7891	1669.5781	0.2182	0.4406
GTRG	44	-790.9308	1669.8617	0.1894	0.6300
GTRIG	45	-790.0878	1670.1756	0.1619	0.7919
HKYI	40	-795.3797	1670.7594	0.1209	0.9128
GTRI	44	-791.7213	1671.4426	0.0859	0.9987
K2PIG	38	-802.9564	1681.9128	0.0005	0.9992
K2PG	37	-804.0395	1682.0790	0.0004	0.9996
K2PI	37	-804.5461	1683.0923	0.0003	0.9999
SYMIG	42	-801.2433	1686.4866	0.0000	0.9999
SYMG	41	-802.2740	1686.5481	0.0000	0.9999
SYMI	41	-802.8868	1687.7735	0.0000	1.0000
GTR	43	-801.9251	1689.8503	0.0000	1.0000
HKY	39	-806.2467	1690.4934	0.0000	1.0000
F81G	39	-806.3302	1690.6603	0.0000	1.0000
F81IG	40	-805.4105	1690.8211	0.0000	1.0000
F81I	39	-806.9129	1691.8257	0.0000	1.0000
JC69G	36	-815.8678	1703.7355	0.0000	1.0000
JC69IG	37	-814.8968	1703.7936	0.0000	1.0000
K2P	36	-816.0418	1704.0836	0.0000	1.0000
JC69I	36	-816.4118	1704.8237	0.0000	1.0000
SYM	40	-813.8063	1707.6125	0.0000	1.0000
F81	38	-817.6852	1711.3703	0.0000	1.0000
JC69	35	-827.4738	1724.9475	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-794.7701	1820.1478	0.3782	0.3782
HKYI	40	-795.3797	1821.3671	0.2056	0.5838
K2PG	37	-804.0395	1821.3911	0.2031	0.7870
K2PI	37	-804.5461	1822.4043	0.1224	0.9094
HKYIG	41	-793.7891	1823.9510	0.0565	0.9659
K2PIG	38	-802.9564	1824.9901	0.0336	0.9995
GTRG	44	-790.9308	1835.5301	0.0002	0.9996
GTRI	44	-791.7213	1837.1110	0.0001	0.9997
HKY	39	-806.2467	1837.3359	0.0001	0.9998
F81G	39	-806.3302	1837.5028	0.0001	0.9998
F81I	39	-806.9129	1838.6682	0.0000	0.9999
JC69G	36	-815.8678	1839.2824	0.0000	0.9999
GTRIG	45	-790.0878	1839.6092	0.0000	0.9999
K2P	36	-816.0418	1839.6304	0.0000	1.0000
JC69I	36	-816.4118	1840.3705	0.0000	1.0000
SYMG	41	-802.2740	1840.9209	0.0000	1.0000
F81IG	40	-805.4105	1841.4287	0.0000	1.0000
SYMI	41	-802.8868	1842.1464	0.0000	1.0000
JC69IG	37	-814.8968	1843.1057	0.0000	1.0000
SYMIG	42	-801.2433	1844.6246	0.0000	1.0000
GTR	43	-801.9251	1851.7535	0.0000	1.0000
F81	38	-817.6852	1854.4476	0.0000	1.0000
JC69	35	-827.4738	1856.7292	0.0000	1.0000
SYM	40	-813.8063	1858.2202	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_13404.phylip = 1 - 319;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_13404.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 AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_13404.phylip = 1 - 319;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_13404.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/chr3_13404.phylip = 1 - 319;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_13404.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

