
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:25 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/chr9_1169.phylip" (19 taxa, 446 characters)

Minimum AIC  model: HKY
Minimum AICc model: HKY
Minimum BIC  model: HKY


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
HKY	39	-883.6325	1852.9496	0.3963	0.3963
HKYI	40	-882.9199	1853.9386	0.2417	0.6379
HKYG	40	-882.9621	1854.0230	0.2317	0.8696
HKYIG	41	-882.9634	1856.4516	0.0688	0.9384
GTR	43	-881.9303	1859.2736	0.0168	0.9552
F81	38	-888.4492	1860.1810	0.0107	0.9659
GTRI	44	-881.2924	1860.4601	0.0093	0.9751
GTRG	44	-881.3168	1860.5090	0.0090	0.9842
F81I	39	-887.8518	1861.3884	0.0058	0.9900
F81G	39	-887.8827	1861.4500	0.0057	0.9957
GTRIG	45	-881.3168	1862.9836	0.0026	0.9983
F81IG	40	-887.8818	1863.8623	0.0017	1.0000
K2P	36	-898.0512	1874.6159	0.0000	1.0000
K2PI	37	-897.3490	1875.5902	0.0000	1.0000
K2PG	37	-897.3964	1875.6849	0.0000	1.0000
K2PIG	38	-897.3975	1878.0776	0.0000	1.0000
SYM	40	-896.1733	1880.4454	0.0000	1.0000
JC69	35	-902.3574	1880.8612	0.0000	1.0000
SYMI	41	-895.5976	1881.7200	0.0000	1.0000
SYMG	41	-895.6327	1881.7903	0.0000	1.0000
JC69I	36	-901.7654	1882.0443	0.0000	1.0000
JC69G	36	-901.8021	1882.1176	0.0000	1.0000
SYMIG	42	-895.6313	1884.2255	0.0000	1.0000
JC69IG	37	-901.8008	1884.4939	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKY	39	-883.6325	1845.2649	0.3275	0.3275
HKYI	40	-882.9199	1845.8399	0.2457	0.5731
HKYG	40	-882.9621	1845.9242	0.2355	0.8087
HKYIG	41	-882.9634	1847.9269	0.0865	0.8952
GTR	43	-881.9303	1849.8606	0.0329	0.9281
GTRI	44	-881.2924	1850.5847	0.0229	0.9510
GTRG	44	-881.3168	1850.6337	0.0224	0.9734
GTRIG	45	-881.3168	1852.6336	0.0082	0.9816
F81	38	-888.4492	1852.8985	0.0072	0.9888
F81I	39	-887.8518	1853.7037	0.0048	0.9936
F81G	39	-887.8827	1853.7653	0.0047	0.9983
F81IG	40	-887.8818	1855.7635	0.0017	1.0000
K2P	36	-898.0512	1868.1024	0.0000	1.0000
K2PI	37	-897.3490	1868.6980	0.0000	1.0000
K2PG	37	-897.3964	1868.7928	0.0000	1.0000
K2PIG	38	-897.3975	1870.7950	0.0000	1.0000
SYM	40	-896.1733	1872.3466	0.0000	1.0000
SYMI	41	-895.5976	1873.1952	0.0000	1.0000
SYMG	41	-895.6327	1873.2655	0.0000	1.0000
JC69	35	-902.3574	1874.7149	0.0000	1.0000
SYMIG	42	-895.6313	1875.2627	0.0000	1.0000
JC69I	36	-901.7654	1875.5309	0.0000	1.0000
JC69G	36	-901.8021	1875.6042	0.0000	1.0000
JC69IG	37	-901.8008	1877.6017	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKY	39	-883.6325	2005.1774	0.7133	0.7133
F81	38	-888.4492	2008.7106	0.1219	0.8352
HKYI	40	-882.9199	2009.8526	0.0689	0.9041
HKYG	40	-882.9621	2009.9370	0.0660	0.9701
F81I	39	-887.8518	2013.6161	0.0105	0.9806
F81G	39	-887.8827	2013.6778	0.0102	0.9908
K2P	36	-898.0512	2015.7139	0.0037	0.9944
HKYIG	41	-882.9634	2016.0400	0.0031	0.9976
JC69	35	-902.3574	2018.2260	0.0010	0.9986
F81IG	40	-887.8818	2019.7763	0.0005	0.9991
K2PI	37	-897.3490	2020.4098	0.0004	0.9994
K2PG	37	-897.3964	2020.5046	0.0003	0.9998
JC69I	36	-901.7654	2023.1423	0.0001	0.9999
JC69G	36	-901.8021	2023.2156	0.0001	1.0000
GTR	43	-881.9303	2026.1743	0.0000	1.0000
K2PIG	38	-897.3975	2026.6071	0.0000	1.0000
JC69IG	37	-901.8008	2029.3135	0.0000	1.0000
GTRI	44	-881.2924	2030.9988	0.0000	1.0000
GTRG	44	-881.3168	2031.0477	0.0000	1.0000
SYM	40	-896.1733	2036.3594	0.0000	1.0000
GTRIG	45	-881.3168	2037.1479	0.0000	1.0000
SYMI	41	-895.5976	2041.3083	0.0000	1.0000
SYMG	41	-895.6327	2041.3786	0.0000	1.0000
SYMIG	42	-895.6313	2047.4761	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_1169.phylip = 1 - 446;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_1169.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_1169.phylip = 1 - 446;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_1169.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_1169.phylip = 1 - 446;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_1169.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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End of Output

