
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:03 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_24662.phylip" (19 taxa, 272 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: HKYI


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	-891.6527	1877.5046	0.3984	0.3984
HKYG	40	-891.8803	1877.9597	0.3173	0.7158
HKYIG	41	-891.6579	1880.2898	0.0990	0.8148
GTRI	44	-887.6663	1880.7775	0.0776	0.8923
GTRG	44	-887.9160	1881.2770	0.0604	0.9527
HKY	39	-895.8726	1883.1935	0.0232	0.9759
GTRIG	45	-887.6711	1883.6608	0.0183	0.9943
GTR	43	-891.8065	1886.2095	0.0051	0.9994
K2PI	37	-902.9948	1892.0066	0.0003	0.9997
K2PG	37	-903.2588	1892.5347	0.0002	0.9999
K2PIG	38	-903.0009	1894.7228	0.0001	1.0000
SYMI	41	-900.7289	1898.4318	0.0000	1.0000
K2P	36	-907.7336	1898.8033	0.0000	1.0000
SYMG	41	-901.0729	1899.1197	0.0000	1.0000
SYMIG	42	-900.7367	1901.2463	0.0000	1.0000
SYM	40	-905.0781	1904.3554	0.0000	1.0000
F81I	39	-910.9259	1913.3001	0.0000	1.0000
F81G	39	-911.1577	1913.7638	0.0000	1.0000
F81IG	40	-910.9317	1916.0625	0.0000	1.0000
F81	38	-915.3916	1919.5042	0.0000	1.0000
JC69I	36	-920.6909	1924.7180	0.0000	1.0000
JC69G	36	-920.9687	1925.2736	0.0000	1.0000
JC69IG	37	-920.6977	1927.4125	0.0000	1.0000
JC69	35	-925.3410	1931.3599	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-891.6527	1863.3055	0.2293	0.2293
GTRI	44	-887.6663	1863.3326	0.2262	0.4554
HKYG	40	-891.8803	1863.7606	0.1826	0.6380
GTRG	44	-887.9160	1863.8321	0.1762	0.8142
HKYIG	41	-891.6579	1865.3159	0.0839	0.8981
GTRIG	45	-887.6711	1865.3422	0.0828	0.9809
GTR	43	-891.8065	1869.6130	0.0098	0.9907
HKY	39	-895.8726	1869.7452	0.0092	0.9999
K2PI	37	-902.9948	1879.9895	0.0001	0.9999
K2PG	37	-903.2588	1880.5176	0.0000	1.0000
K2PIG	38	-903.0009	1882.0017	0.0000	1.0000
SYMI	41	-900.7289	1883.4579	0.0000	1.0000
SYMG	41	-901.0729	1884.1458	0.0000	1.0000
SYMIG	42	-900.7367	1885.4734	0.0000	1.0000
K2P	36	-907.7336	1887.4671	0.0000	1.0000
SYM	40	-905.0781	1890.1562	0.0000	1.0000
F81I	39	-910.9259	1899.8519	0.0000	1.0000
F81G	39	-911.1577	1900.3155	0.0000	1.0000
F81IG	40	-910.9317	1901.8634	0.0000	1.0000
F81	38	-915.3916	1906.7832	0.0000	1.0000
JC69I	36	-920.6909	1913.3818	0.0000	1.0000
JC69G	36	-920.9687	1913.9375	0.0000	1.0000
JC69IG	37	-920.6977	1915.3954	0.0000	1.0000
JC69	35	-925.3410	1920.6819	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-891.6527	2007.5375	0.4534	0.4534
HKYG	40	-891.8803	2007.9927	0.3611	0.8144
HKY	39	-895.8726	2010.3715	0.1099	0.9244
HKYIG	41	-891.6579	2013.1538	0.0273	0.9517
K2PI	37	-902.9948	2013.4042	0.0241	0.9758
K2PG	37	-903.2588	2013.9323	0.0185	0.9944
K2P	36	-907.7336	2017.2760	0.0035	0.9978
K2PIG	38	-903.0009	2019.0222	0.0015	0.9993
GTRI	44	-887.6663	2021.9879	0.0003	0.9996
GTRG	44	-887.9160	2022.4874	0.0003	0.9999
GTR	43	-891.8065	2024.6625	0.0001	1.0000
GTRIG	45	-887.6711	2027.6033	0.0000	1.0000
SYMI	41	-900.7289	2031.2958	0.0000	1.0000
SYMG	41	-901.0729	2031.9836	0.0000	1.0000
SYM	40	-905.0781	2034.3883	0.0000	1.0000
SYMIG	42	-900.7367	2036.9171	0.0000	1.0000
F81I	39	-910.9259	2040.4781	0.0000	1.0000
F81G	39	-911.1577	2040.9418	0.0000	1.0000
JC69I	36	-920.6909	2043.1907	0.0000	1.0000
JC69G	36	-920.9687	2043.7463	0.0000	1.0000
F81	38	-915.3916	2043.8036	0.0000	1.0000
F81IG	40	-910.9317	2046.0955	0.0000	1.0000
JC69	35	-925.3410	2046.8850	0.0000	1.0000
JC69IG	37	-920.6977	2048.8101	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/chr2_24662.phylip = 1 - 272;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24662.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/chr2_24662.phylip = 1 - 272;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24662.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 (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24662.phylip = 1 - 272;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24662.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;


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End of Output

