
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:04 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_4395.phylip" (19 taxa, 345 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	-830.8186	1752.4266	0.2641	0.2641
HKYI	40	-830.8934	1752.5764	0.2451	0.5092
GTRG	44	-825.9804	1753.1608	0.1830	0.6922
GTRI	44	-826.0308	1753.2617	0.1740	0.8662
HKYIG	41	-830.6835	1754.7334	0.0834	0.9495
GTRIG	45	-825.9458	1755.7379	0.0504	1.0000
HKY	39	-842.4259	1773.0814	0.0000	1.0000
GTR	43	-837.8444	1774.2603	0.0000	1.0000
F81G	39	-845.4280	1779.0855	0.0000	1.0000
F81I	39	-845.5000	1779.2295	0.0000	1.0000
F81IG	40	-845.2470	1781.2836	0.0000	1.0000
K2PG	37	-849.2230	1781.6057	0.0000	1.0000
K2PI	37	-849.2971	1781.7537	0.0000	1.0000
K2PIG	38	-848.9613	1783.6088	0.0000	1.0000
SYMG	41	-846.5669	1786.5002	0.0000	1.0000
SYMI	41	-846.5952	1786.5567	0.0000	1.0000
SYMIG	42	-846.4999	1788.9601	0.0000	1.0000
F81	38	-857.2327	1800.1516	0.0000	1.0000
K2P	36	-861.2759	1803.2012	0.0000	1.0000
JC69G	36	-862.0167	1804.6827	0.0000	1.0000
JC69I	36	-862.0968	1804.8429	0.0000	1.0000
JC69IG	37	-861.7443	1806.6482	0.0000	1.0000
SYM	40	-858.6123	1808.0142	0.0000	1.0000
JC69	35	-874.0038	1826.1629	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-825.9804	1739.9608	0.2987	0.2987
GTRI	44	-826.0308	1740.0617	0.2840	0.5828
HKYG	40	-830.8186	1741.6372	0.1292	0.7120
HKYI	40	-830.8934	1741.7869	0.1199	0.8318
GTRIG	45	-825.9458	1741.8917	0.1138	0.9456
HKYIG	41	-830.6835	1743.3670	0.0544	1.0000
GTR	43	-837.8444	1761.6889	0.0000	1.0000
HKY	39	-842.4259	1762.8519	0.0000	1.0000
F81G	39	-845.4280	1768.8560	0.0000	1.0000
F81I	39	-845.5000	1769.0000	0.0000	1.0000
F81IG	40	-845.2470	1770.4941	0.0000	1.0000
K2PG	37	-849.2230	1772.4461	0.0000	1.0000
K2PI	37	-849.2971	1772.5941	0.0000	1.0000
K2PIG	38	-848.9613	1773.9226	0.0000	1.0000
SYMG	41	-846.5669	1775.1339	0.0000	1.0000
SYMI	41	-846.5952	1775.1904	0.0000	1.0000
SYMIG	42	-846.4999	1776.9999	0.0000	1.0000
F81	38	-857.2327	1790.4654	0.0000	1.0000
K2P	36	-861.2759	1794.5518	0.0000	1.0000
JC69G	36	-862.0167	1796.0334	0.0000	1.0000
JC69I	36	-862.0968	1796.1935	0.0000	1.0000
SYM	40	-858.6123	1797.2247	0.0000	1.0000
JC69IG	37	-861.7443	1797.4886	0.0000	1.0000
JC69	35	-874.0038	1818.0076	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-830.8186	1895.3789	0.5020	0.5020
HKYI	40	-830.8934	1895.5287	0.4658	0.9678
HKYIG	41	-830.6835	1900.9524	0.0309	0.9988
GTRG	44	-825.9804	1909.0767	0.0005	0.9993
GTRI	44	-826.0308	1909.1776	0.0005	0.9998
HKY	39	-842.4259	1912.7501	0.0001	0.9999
K2PG	37	-849.2230	1914.6572	0.0000	0.9999
K2PI	37	-849.2971	1914.8053	0.0000	1.0000
GTRIG	45	-825.9458	1914.8512	0.0000	1.0000
F81G	39	-845.4280	1918.7542	0.0000	1.0000
F81I	39	-845.5000	1918.8983	0.0000	1.0000
K2PIG	38	-848.9613	1919.9772	0.0000	1.0000
F81IG	40	-845.2470	1924.2359	0.0000	1.0000
GTR	43	-837.8444	1926.9613	0.0000	1.0000
SYMG	41	-846.5669	1932.7192	0.0000	1.0000
SYMI	41	-846.5952	1932.7757	0.0000	1.0000
K2P	36	-861.2759	1932.9194	0.0000	1.0000
JC69G	36	-862.0167	1934.4010	0.0000	1.0000
JC69I	36	-862.0968	1934.5611	0.0000	1.0000
F81	38	-857.2327	1936.5200	0.0000	1.0000
SYMIG	42	-846.4999	1938.4287	0.0000	1.0000
JC69IG	37	-861.7443	1939.6998	0.0000	1.0000
SYM	40	-858.6123	1950.9665	0.0000	1.0000
JC69	35	-874.0038	1952.5317	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_4395.phylip = 1 - 345;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_4395.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_4395.phylip = 1 - 345;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_4395.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_4395.phylip = 1 - 345;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_4395.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

