
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/chr4_17854.phylip" (19 taxa, 259 characters)

Minimum AIC  model: GTRI
Minimum AICc model: K2PG
Minimum BIC  model: K2PG


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
K2PG	37	-791.1986	1669.1211	0.2983	0.2983
GTRI	44	-782.1323	1670.7694	0.1308	0.4291
GTRG	44	-782.2635	1671.0316	0.1148	0.5439
K2PI	37	-792.1757	1671.0754	0.1123	0.6561
SYMG	41	-786.8686	1671.6082	0.0860	0.7421
HKYI	40	-788.4158	1671.8775	0.0752	0.8173
HKYG	40	-788.5631	1672.1720	0.0649	0.8822
GTRIG	45	-781.7720	1672.9805	0.0433	0.9255
SYMI	41	-788.0440	1673.9589	0.0266	0.9521
HKYIG	41	-788.1942	1674.2594	0.0228	0.9749
K2PIG	38	-792.4774	1674.4275	0.0210	0.9959
SYMIG	42	-788.4917	1677.7055	0.0041	1.0000
JC69G	36	-802.9440	1689.8881	0.0000	1.0000
JC69I	36	-804.0303	1692.0607	0.0000	1.0000
F81I	39	-800.9066	1694.0597	0.0000	1.0000
F81G	39	-801.0774	1694.4013	0.0000	1.0000
JC69IG	37	-804.2146	1695.1531	0.0000	1.0000
F81IG	40	-801.0771	1697.2000	0.0000	1.0000
K2P	36	-809.1037	1702.2073	0.0000	1.0000
GTR	43	-799.3593	1702.3185	0.0000	1.0000
HKY	39	-805.0639	1702.3744	0.0000	1.0000
SYM	40	-803.9918	1703.0296	0.0000	1.0000
JC69	35	-820.6104	1722.5213	0.0000	1.0000
F81	38	-817.4091	1724.2909	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-782.1323	1652.2647	0.3255	0.3255
GTRG	44	-782.2635	1652.5269	0.2855	0.6110
GTRIG	45	-781.7720	1653.5439	0.1717	0.7828
SYMG	41	-786.8686	1655.7372	0.0574	0.8401
K2PG	37	-791.1986	1656.3971	0.0412	0.8813
HKYI	40	-788.4158	1656.8316	0.0332	0.9145
HKYG	40	-788.5631	1657.1262	0.0286	0.9432
SYMI	41	-788.0440	1658.0879	0.0177	0.9609
K2PI	37	-792.1757	1658.3514	0.0155	0.9764
HKYIG	41	-788.1942	1658.3884	0.0152	0.9916
K2PIG	38	-792.4774	1660.9548	0.0042	0.9958
SYMIG	42	-788.4917	1660.9833	0.0042	1.0000
JC69G	36	-802.9440	1677.8881	0.0000	1.0000
F81I	39	-800.9066	1679.8132	0.0000	1.0000
JC69I	36	-804.0303	1680.0607	0.0000	1.0000
F81G	39	-801.0774	1680.1547	0.0000	1.0000
F81IG	40	-801.0771	1682.1541	0.0000	1.0000
JC69IG	37	-804.2146	1682.4291	0.0000	1.0000
GTR	43	-799.3593	1684.7185	0.0000	1.0000
SYM	40	-803.9918	1687.9837	0.0000	1.0000
HKY	39	-805.0639	1688.1278	0.0000	1.0000
K2P	36	-809.1037	1690.2073	0.0000	1.0000
F81	38	-817.4091	1710.8182	0.0000	1.0000
JC69	35	-820.6104	1711.2208	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-791.1986	1787.9998	0.7128	0.7128
K2PI	37	-792.1757	1789.9541	0.2683	0.9811
K2PIG	38	-792.4774	1796.1142	0.0123	0.9934
HKYI	40	-788.4158	1799.1047	0.0028	0.9962
HKYG	40	-788.5631	1799.3993	0.0024	0.9986
SYMG	41	-786.8686	1801.5672	0.0008	0.9994
SYMI	41	-788.0440	1803.9179	0.0002	0.9996
HKYIG	41	-788.1942	1804.2184	0.0002	0.9998
JC69G	36	-802.9440	1805.9339	0.0001	0.9999
JC69I	36	-804.0303	1808.1065	0.0000	0.9999
GTRI	44	-782.1323	1808.7651	0.0000	1.0000
GTRG	44	-782.2635	1809.0274	0.0000	1.0000
SYMIG	42	-788.4917	1810.3701	0.0000	1.0000
GTRIG	45	-781.7720	1813.6012	0.0000	1.0000
JC69IG	37	-804.2146	1814.0318	0.0000	1.0000
K2P	36	-809.1037	1818.2531	0.0000	1.0000
F81I	39	-800.9066	1818.5295	0.0000	1.0000
F81G	39	-801.0774	1818.8710	0.0000	1.0000
F81IG	40	-801.0771	1824.4273	0.0000	1.0000
HKY	39	-805.0639	1826.8441	0.0000	1.0000
SYM	40	-803.9918	1830.2568	0.0000	1.0000
JC69	35	-820.6104	1835.7098	0.0000	1.0000
GTR	43	-799.3593	1837.6621	0.0000	1.0000
F81	38	-817.4091	1845.9776	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_17854.phylip = 1 - 259;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_17854.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_17854.phylip = 1 - 259;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_17854.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_17854.phylip = 1 - 259;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_17854.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

