
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:21 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/chr4_16780.phylip" (19 taxa, 302 characters)

Minimum AIC  model: SYMI
Minimum AICc model: SYMI
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
SYMI	41	-805.5355	1706.3172	0.7350	0.7350
K2PI	37	-812.8971	1710.4458	0.0933	0.8283
K2PIG	38	-812.0848	1711.4395	0.0568	0.8850
SYMIG	42	-807.1379	1712.2217	0.0384	0.9234
K2PG	37	-813.9204	1712.4923	0.0335	0.9570
SYMG	41	-809.1430	1713.5322	0.0199	0.9769
GTRI	44	-805.9853	1715.3792	0.0079	0.9848
GTRG	44	-806.2451	1715.8987	0.0061	0.9909
HKYI	40	-812.3222	1717.2114	0.0032	0.9941
GTRIG	45	-805.5847	1717.3412	0.0030	0.9970
HKYIG	41	-811.5161	1718.2784	0.0019	0.9989
HKYG	40	-813.3815	1719.3300	0.0011	1.0000
JC69I	36	-834.7552	1751.5632	0.0000	1.0000
JC69G	36	-834.9956	1752.0441	0.0000	1.0000
JC69IG	37	-833.8213	1752.2941	0.0000	1.0000
F81I	39	-834.0467	1758.0019	0.0000	1.0000
F81G	39	-834.2027	1758.3139	0.0000	1.0000
F81IG	40	-833.1893	1758.9456	0.0000	1.0000
GTR	43	-839.7436	1780.1539	0.0000	1.0000
K2P	36	-849.8792	1781.8112	0.0000	1.0000
SYM	40	-844.9583	1782.4835	0.0000	1.0000
HKY	39	-849.0751	1788.0586	0.0000	1.0000
JC69	35	-869.2519	1817.9774	0.0000	1.0000
F81	38	-868.1950	1823.6600	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
SYMI	41	-805.5355	1693.0710	0.7953	0.7953
SYMIG	42	-807.1379	1698.2758	0.0589	0.8542
K2PI	37	-812.8971	1699.7943	0.0276	0.8818
GTRI	44	-805.9853	1699.9707	0.0253	0.9070
K2PIG	38	-812.0848	1700.1695	0.0229	0.9299
SYMG	41	-809.1430	1700.2861	0.0216	0.9514
GTRG	44	-806.2451	1700.4902	0.0195	0.9709
GTRIG	45	-805.5847	1701.1694	0.0139	0.9848
K2PG	37	-813.9204	1701.8408	0.0099	0.9947
HKYI	40	-812.3222	1704.6444	0.0024	0.9971
HKYIG	41	-811.5161	1705.0322	0.0020	0.9992
HKYG	40	-813.3815	1706.7629	0.0008	1.0000
JC69I	36	-834.7552	1741.5103	0.0000	1.0000
JC69IG	37	-833.8213	1741.6425	0.0000	1.0000
JC69G	36	-834.9956	1741.9912	0.0000	1.0000
F81I	39	-834.0467	1746.0935	0.0000	1.0000
F81IG	40	-833.1893	1746.3785	0.0000	1.0000
F81G	39	-834.2027	1746.4055	0.0000	1.0000
GTR	43	-839.7436	1765.4873	0.0000	1.0000
SYM	40	-844.9583	1769.9165	0.0000	1.0000
K2P	36	-849.8792	1771.7584	0.0000	1.0000
HKY	39	-849.0751	1776.1502	0.0000	1.0000
JC69	35	-869.2519	1808.5037	0.0000	1.0000
F81	38	-868.1950	1812.3901	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-812.8971	1837.0801	0.6633	0.6633
K2PG	37	-813.9204	1839.1266	0.2384	0.9018
K2PIG	38	-812.0848	1841.1657	0.0860	0.9878
SYMI	41	-805.5355	1845.1985	0.0115	0.9992
SYMG	41	-809.1430	1852.4136	0.0003	0.9995
HKYI	40	-812.3222	1853.0615	0.0002	0.9998
SYMIG	42	-807.1379	1854.1137	0.0001	0.9999
HKYG	40	-813.3815	1855.1800	0.0001	1.0000
HKYIG	41	-811.5161	1857.1597	0.0000	1.0000
GTRI	44	-805.9853	1863.2294	0.0000	1.0000
GTRG	44	-806.2451	1863.7490	0.0000	1.0000
GTRIG	45	-805.5847	1868.1386	0.0000	1.0000
JC69I	36	-834.7552	1875.0857	0.0000	1.0000
JC69G	36	-834.9956	1875.5666	0.0000	1.0000
JC69IG	37	-833.8213	1878.9283	0.0000	1.0000
F81I	39	-834.0467	1890.8002	0.0000	1.0000
F81G	39	-834.2027	1891.1121	0.0000	1.0000
F81IG	40	-833.1893	1894.7956	0.0000	1.0000
K2P	36	-849.8792	1905.3337	0.0000	1.0000
SYM	40	-844.9583	1918.3336	0.0000	1.0000
HKY	39	-849.0751	1920.8568	0.0000	1.0000
GTR	43	-839.7436	1925.0356	0.0000	1.0000
JC69	35	-869.2519	1938.3687	0.0000	1.0000
F81	38	-868.1950	1953.3863	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_16780.phylip = 1 - 302;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_16780.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=Fixed(Equal) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_16780.phylip = 1 - 302;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_16780.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=Fixed(Equal) 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/chr4_16780.phylip = 1 - 302;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_16780.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

