
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:59 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/chr6_6012.phylip" (19 taxa, 366 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	-807.6421	1705.3764	0.2676	0.2676
HKYI	40	-807.7115	1705.5153	0.2497	0.5173
GTRG	44	-802.9555	1706.2475	0.1731	0.6905
GTRI	44	-803.2228	1706.7819	0.1325	0.8230
HKYIG	41	-807.2535	1707.1366	0.1110	0.9340
GTRIG	45	-802.6346	1708.2068	0.0650	0.9990
GTR	43	-809.7705	1717.2926	0.0007	0.9997
HKY	39	-815.8388	1719.2482	0.0003	1.0000
F81G	39	-818.7277	1725.0259	0.0000	1.0000
F81I	39	-818.7752	1725.1209	0.0000	1.0000
F81IG	40	-818.3086	1726.7096	0.0000	1.0000
F81	38	-827.0873	1739.2388	0.0000	1.0000
K2PI	37	-829.9071	1742.3873	0.0000	1.0000
K2PG	37	-829.9765	1742.5261	0.0000	1.0000
K2PIG	38	-829.3157	1743.6955	0.0000	1.0000
SYMG	41	-825.7566	1744.1428	0.0000	1.0000
SYMI	41	-825.8131	1744.2558	0.0000	1.0000
SYMIG	42	-825.1144	1745.4115	0.0000	1.0000
SYM	40	-834.2450	1758.5823	0.0000	1.0000
K2P	36	-839.4500	1758.9973	0.0000	1.0000
JC69I	36	-839.8087	1759.7146	0.0000	1.0000
JC69G	36	-839.8256	1759.7484	0.0000	1.0000
JC69IG	37	-839.2812	1761.1356	0.0000	1.0000
JC69	35	-848.8642	1775.3648	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-802.9555	1693.9111	0.2839	0.2839
GTRI	44	-803.2228	1694.4455	0.2174	0.5013
GTRIG	45	-802.6346	1695.2693	0.1440	0.6453
HKYG	40	-807.6421	1695.2841	0.1429	0.7882
HKYI	40	-807.7115	1695.4230	0.1333	0.9215
HKYIG	41	-807.2535	1696.5069	0.0775	0.9990
GTR	43	-809.7705	1705.5410	0.0008	0.9999
HKY	39	-815.8388	1709.6776	0.0001	1.0000
F81G	39	-818.7277	1715.4554	0.0000	1.0000
F81I	39	-818.7752	1715.5503	0.0000	1.0000
F81IG	40	-818.3086	1716.6173	0.0000	1.0000
F81	38	-827.0873	1730.1746	0.0000	1.0000
SYMG	41	-825.7566	1733.5131	0.0000	1.0000
SYMI	41	-825.8131	1733.6262	0.0000	1.0000
K2PI	37	-829.9071	1733.8141	0.0000	1.0000
K2PG	37	-829.9765	1733.9529	0.0000	1.0000
SYMIG	42	-825.1144	1734.2289	0.0000	1.0000
K2PIG	38	-829.3157	1734.6313	0.0000	1.0000
SYM	40	-834.2450	1748.4900	0.0000	1.0000
K2P	36	-839.4500	1750.9000	0.0000	1.0000
JC69I	36	-839.8087	1751.6173	0.0000	1.0000
JC69G	36	-839.8256	1751.6511	0.0000	1.0000
JC69IG	37	-839.2812	1752.5624	0.0000	1.0000
JC69	35	-848.8642	1767.7285	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-807.6421	1851.3895	0.4957	0.4957
HKYI	40	-807.7115	1851.5284	0.4624	0.9581
HKYIG	41	-807.2535	1856.5149	0.0382	0.9963
HKY	39	-815.8388	1861.8803	0.0026	0.9990
GTRG	44	-802.9555	1865.6269	0.0004	0.9994
GTRI	44	-803.2228	1866.1614	0.0003	0.9997
F81G	39	-818.7277	1867.6581	0.0001	0.9998
F81I	39	-818.7752	1867.7530	0.0001	0.9999
GTRIG	45	-802.6346	1870.8878	0.0000	1.0000
F81IG	40	-818.3086	1872.7226	0.0000	1.0000
GTR	43	-809.7705	1873.3542	0.0000	1.0000
K2PI	37	-829.9071	1878.2115	0.0000	1.0000
K2PG	37	-829.9765	1878.3504	0.0000	1.0000
F81	38	-827.0873	1878.4746	0.0000	1.0000
K2PIG	38	-829.3157	1882.9314	0.0000	1.0000
K2P	36	-839.4500	1891.3948	0.0000	1.0000
JC69I	36	-839.8087	1892.1121	0.0000	1.0000
JC69G	36	-839.8256	1892.1459	0.0000	1.0000
SYMG	41	-825.7566	1893.5211	0.0000	1.0000
SYMI	41	-825.8131	1893.6341	0.0000	1.0000
JC69IG	37	-839.2812	1896.9599	0.0000	1.0000
SYMIG	42	-825.1144	1898.1395	0.0000	1.0000
JC69	35	-848.8642	1904.3206	0.0000	1.0000
SYM	40	-834.2450	1904.5953	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/chr6_6012.phylip = 1 - 366;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_6012.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/chr6_6012.phylip = 1 - 366;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_6012.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/chr6_6012.phylip = 1 - 366;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_6012.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

