
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:16 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_5476.phylip" (19 taxa, 362 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	-859.4721	1809.1623	0.2629	0.2629
HKYG	40	-859.5268	1809.2717	0.2489	0.5117
GTRI	44	-854.7814	1810.0549	0.1682	0.6800
GTRG	44	-854.7988	1810.0898	0.1653	0.8453
HKYIG	41	-859.5264	1811.8152	0.0698	0.9150
GTRIG	45	-854.7950	1812.6912	0.0450	0.9601
K2PI	37	-866.0856	1814.8502	0.0153	0.9754
K2PG	37	-866.1812	1815.0413	0.0139	0.9893
K2PIG	38	-866.1809	1817.5383	0.0040	0.9932
SYMI	41	-862.6719	1818.1064	0.0030	0.9963
SYMG	41	-862.7385	1818.2396	0.0028	0.9991
SYMIG	42	-862.7383	1820.7995	0.0008	0.9998
HKY	39	-868.4764	1824.6423	0.0001	1.0000
GTR	43	-864.6916	1827.2826	0.0000	1.0000
K2P	36	-874.5572	1829.3113	0.0000	1.0000
SYM	40	-871.6143	1833.4468	0.0000	1.0000
F81I	39	-873.7800	1835.2495	0.0000	1.0000
F81G	39	-873.8677	1835.4249	0.0000	1.0000
F81IG	40	-873.8675	1837.9531	0.0000	1.0000
JC69I	36	-879.2390	1838.6750	0.0000	1.0000
JC69G	36	-879.3456	1838.8882	0.0000	1.0000
JC69IG	37	-879.3454	1841.3699	0.0000	1.0000
F81	38	-881.9371	1849.0507	0.0000	1.0000
JC69	35	-887.2141	1852.1582	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-854.7814	1797.5628	0.2822	0.2822
GTRG	44	-854.7988	1797.5976	0.2773	0.5595
HKYI	40	-859.4721	1798.9442	0.1414	0.7009
HKYG	40	-859.5268	1799.0537	0.1339	0.8348
GTRIG	45	-854.7950	1799.5900	0.1024	0.9372
HKYIG	41	-859.5264	1801.0527	0.0493	0.9865
K2PI	37	-866.0856	1806.1712	0.0038	0.9903
K2PG	37	-866.1812	1806.3623	0.0035	0.9938
SYMI	41	-862.6719	1807.3439	0.0021	0.9959
SYMG	41	-862.7385	1807.4771	0.0020	0.9979
K2PIG	38	-866.1809	1808.3618	0.0013	0.9992
SYMIG	42	-862.7383	1809.4766	0.0007	0.9999
HKY	39	-868.4764	1814.9529	0.0000	1.0000
GTR	43	-864.6916	1815.3833	0.0000	1.0000
K2P	36	-874.5572	1821.1144	0.0000	1.0000
SYM	40	-871.6143	1823.2287	0.0000	1.0000
F81I	39	-873.7800	1825.5600	0.0000	1.0000
F81G	39	-873.8677	1825.7355	0.0000	1.0000
F81IG	40	-873.8675	1827.7350	0.0000	1.0000
JC69I	36	-879.2390	1830.4781	0.0000	1.0000
JC69G	36	-879.3456	1830.6913	0.0000	1.0000
JC69IG	37	-879.3454	1832.6909	0.0000	1.0000
F81	38	-881.9371	1839.8742	0.0000	1.0000
JC69	35	-887.2141	1844.4281	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-866.0856	1950.1620	0.4592	0.4592
K2PG	37	-866.1812	1950.3532	0.4174	0.8766
HKYI	40	-859.4721	1954.6100	0.0497	0.9263
HKYG	40	-859.5268	1954.7194	0.0470	0.9733
K2PIG	38	-866.1809	1956.2443	0.0219	0.9953
HKYIG	41	-859.5264	1960.6102	0.0025	0.9977
K2P	36	-874.5572	1961.2136	0.0018	0.9996
HKY	39	-868.4764	1966.7270	0.0001	0.9997
SYMI	41	-862.6719	1966.9013	0.0001	0.9998
SYMG	41	-862.7385	1967.0345	0.0001	0.9999
GTRI	44	-854.7814	1968.7951	0.0000	0.9999
GTRG	44	-854.7988	1968.8300	0.0000	1.0000
JC69I	36	-879.2390	1970.5773	0.0000	1.0000
JC69G	36	-879.3456	1970.7905	0.0000	1.0000
SYMIG	42	-862.7383	1972.9257	0.0000	1.0000
GTRIG	45	-854.7950	1974.7139	0.0000	1.0000
JC69IG	37	-879.3454	1976.6817	0.0000	1.0000
F81I	39	-873.7800	1977.3341	0.0000	1.0000
F81G	39	-873.8677	1977.5096	0.0000	1.0000
SYM	40	-871.6143	1978.8945	0.0000	1.0000
JC69	35	-887.2141	1980.6356	0.0000	1.0000
GTR	43	-864.6916	1982.7240	0.0000	1.0000
F81IG	40	-873.8675	1983.4008	0.0000	1.0000
F81	38	-881.9371	1987.7567	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_5476.phylip = 1 - 362;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5476.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_5476.phylip = 1 - 362;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5476.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_5476.phylip = 1 - 362;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5476.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

