
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:05 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_3180.phylip" (19 taxa, 335 characters)

Minimum AIC  model: GTRI
Minimum AICc model: HKYI
Minimum BIC  model: K2PI


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	-857.9625	1807.0815	0.3211	0.3211
HKYG	40	-858.4332	1808.0228	0.2006	0.5216
HKYIG	41	-857.2456	1808.2455	0.1794	0.7011
GTRI	44	-853.5766	1808.8083	0.1354	0.8365
GTRG	44	-854.0698	1809.7947	0.0827	0.9192
GTRIG	45	-852.9399	1810.2051	0.0674	0.9865
K2PI	37	-865.8973	1815.2626	0.0054	0.9919
K2PG	37	-866.4588	1816.3856	0.0031	0.9950
K2PIG	38	-865.4257	1816.8649	0.0024	0.9974
SYMI	41	-862.1498	1818.0538	0.0013	0.9987
SYMG	41	-862.7996	1819.3534	0.0007	0.9994
SYMIG	42	-861.8730	1820.1159	0.0005	0.9999
F81I	39	-867.8378	1824.2519	0.0001	0.9999
F81G	39	-868.3333	1825.2428	0.0000	1.0000
F81IG	40	-867.2300	1825.6164	0.0000	1.0000
JC69I	36	-875.4120	1831.7636	0.0000	1.0000
JC69G	36	-875.9455	1832.8306	0.0000	1.0000
JC69IG	37	-874.8634	1833.1948	0.0000	1.0000
HKY	39	-882.1753	1852.9269	0.0000	1.0000
GTR	43	-878.5421	1856.0877	0.0000	1.0000
K2P	36	-890.4746	1861.8888	0.0000	1.0000
SYM	40	-887.4172	1865.9908	0.0000	1.0000
F81	38	-892.0703	1870.1542	0.0000	1.0000
JC69	35	-899.8154	1878.0589	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-853.5766	1795.1531	0.2537	0.2537
GTRIG	45	-852.9399	1795.8799	0.1764	0.4302
HKYI	40	-857.9625	1795.9250	0.1725	0.6027
GTRG	44	-854.0698	1796.1396	0.1550	0.7576
HKYIG	41	-857.2456	1796.4913	0.1300	0.8876
HKYG	40	-858.4332	1796.8664	0.1077	0.9953
K2PI	37	-865.8973	1805.7946	0.0012	0.9966
SYMI	41	-862.1498	1806.2996	0.0010	0.9975
K2PIG	38	-865.4257	1806.8513	0.0007	0.9983
K2PG	37	-866.4588	1806.9176	0.0007	0.9990
SYMG	41	-862.7996	1807.5992	0.0005	0.9995
SYMIG	42	-861.8730	1807.7460	0.0005	0.9999
F81I	39	-867.8378	1813.6756	0.0000	1.0000
F81IG	40	-867.2300	1814.4599	0.0000	1.0000
F81G	39	-868.3333	1814.6665	0.0000	1.0000
JC69I	36	-875.4120	1822.8240	0.0000	1.0000
JC69IG	37	-874.8634	1823.7268	0.0000	1.0000
JC69G	36	-875.9455	1823.8910	0.0000	1.0000
HKY	39	-882.1753	1842.3506	0.0000	1.0000
GTR	43	-878.5421	1843.0842	0.0000	1.0000
K2P	36	-890.4746	1852.9492	0.0000	1.0000
SYM	40	-887.4172	1854.8343	0.0000	1.0000
F81	38	-892.0703	1860.1407	0.0000	1.0000
JC69	35	-899.8154	1869.6308	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-865.8973	1946.9174	0.4077	0.4077
K2PG	37	-866.4588	1948.0404	0.2325	0.6402
HKYI	40	-857.9625	1948.4903	0.1857	0.8259
HKYG	40	-858.4332	1949.4316	0.1160	0.9418
K2PIG	38	-865.4257	1951.7883	0.0357	0.9775
HKYIG	41	-857.2456	1952.8706	0.0208	0.9983
JC69I	36	-875.4120	1960.1327	0.0006	0.9989
JC69G	36	-875.9455	1961.1997	0.0003	0.9992
F81I	39	-867.8378	1962.4267	0.0002	0.9994
SYMI	41	-862.1498	1962.6789	0.0002	0.9995
GTRI	44	-853.5766	1962.9749	0.0001	0.9996
F81G	39	-868.3333	1963.4176	0.0001	0.9997
GTRG	44	-854.0698	1963.9613	0.0001	0.9998
SYMG	41	-862.7996	1963.9785	0.0001	0.9999
JC69IG	37	-874.8634	1964.8496	0.0001	1.0000
F81IG	40	-867.2300	1967.0252	0.0000	1.0000
GTRIG	45	-852.9399	1967.5158	0.0000	1.0000
SYMIG	42	-861.8730	1967.9395	0.0000	1.0000
K2P	36	-890.4746	1990.2579	0.0000	1.0000
HKY	39	-882.1753	1991.1017	0.0000	1.0000
JC69	35	-899.8154	2003.1253	0.0000	1.0000
F81	38	-892.0703	2005.0776	0.0000	1.0000
GTR	43	-878.5421	2007.0918	0.0000	1.0000
SYM	40	-887.4172	2007.3995	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/chr3_3180.phylip = 1 - 335;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3180.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 (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3180.phylip = 1 - 335;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3180.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 (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3180.phylip = 1 - 335;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3180.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

