
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:50 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_25984.phylip" (19 taxa, 286 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
Minimum BIC  model: HKY


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
GTRI	44	-742.7322	1589.8959	0.2056	0.2056
GTR	43	-744.2112	1590.0587	0.1896	0.3952
GTRG	44	-743.0406	1590.5127	0.1511	0.5463
HKYI	40	-748.6237	1590.6352	0.1421	0.6883
HKY	39	-750.1672	1591.0174	0.1174	0.8057
HKYG	40	-748.8951	1591.1780	0.1083	0.9140
GTRIG	45	-742.7415	1592.7331	0.0498	0.9638
HKYIG	41	-748.6317	1593.3782	0.0361	0.9999
K2PI	37	-760.6847	1606.7081	0.0000	0.9999
K2P	36	-762.1763	1607.0514	0.0000	0.9999
K2PG	37	-760.9959	1607.3306	0.0000	1.0000
K2PIG	38	-760.6940	1609.3881	0.0000	1.0000
SYMI	41	-757.6166	1611.3479	0.0000	1.0000
SYM	40	-758.9923	1611.3723	0.0000	1.0000
SYMG	41	-757.9561	1612.0270	0.0000	1.0000
SYMIG	42	-757.6271	1614.1183	0.0000	1.0000
F81	38	-764.7741	1617.5482	0.0000	1.0000
F81I	39	-763.4792	1617.6414	0.0000	1.0000
F81G	39	-763.7496	1618.1822	0.0000	1.0000
F81IG	40	-763.4880	1620.3637	0.0000	1.0000
JC69I	36	-775.4613	1633.6214	0.0000	1.0000
JC69	35	-776.8263	1633.7325	0.0000	1.0000
JC69G	36	-775.7571	1634.2130	0.0000	1.0000
JC69IG	37	-775.4704	1636.2794	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-742.7322	1573.4643	0.3198	0.3198
GTRG	44	-743.0406	1574.0812	0.2349	0.5547
GTR	43	-744.2112	1574.4224	0.1981	0.7528
GTRIG	45	-742.7415	1575.4831	0.1166	0.8694
HKYI	40	-748.6237	1577.2474	0.0482	0.9176
HKYG	40	-748.8951	1577.7903	0.0368	0.9544
HKY	39	-750.1672	1578.3345	0.0280	0.9824
HKYIG	41	-748.6317	1579.2634	0.0176	1.0000
K2PI	37	-760.6847	1595.3694	0.0000	1.0000
K2PG	37	-760.9959	1595.9919	0.0000	1.0000
K2P	36	-762.1763	1596.3526	0.0000	1.0000
SYMI	41	-757.6166	1597.2331	0.0000	1.0000
K2PIG	38	-760.6940	1597.3881	0.0000	1.0000
SYMG	41	-757.9561	1597.9122	0.0000	1.0000
SYM	40	-758.9923	1597.9845	0.0000	1.0000
SYMIG	42	-757.6271	1599.2541	0.0000	1.0000
F81I	39	-763.4792	1604.9584	0.0000	1.0000
F81G	39	-763.7496	1605.4993	0.0000	1.0000
F81	38	-764.7741	1605.5482	0.0000	1.0000
F81IG	40	-763.4880	1606.9760	0.0000	1.0000
JC69I	36	-775.4613	1622.9226	0.0000	1.0000
JC69G	36	-775.7571	1623.5142	0.0000	1.0000
JC69	35	-776.8263	1623.6525	0.0000	1.0000
JC69IG	37	-775.4704	1624.9407	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKY	39	-750.1672	1720.9181	0.6434	0.6434
HKYI	40	-748.6237	1723.4871	0.1781	0.8215
HKYG	40	-748.8951	1724.0300	0.1358	0.9572
K2P	36	-762.1763	1727.9683	0.0189	0.9762
HKYIG	41	-748.6317	1729.1591	0.0104	0.9866
K2PI	37	-760.6847	1730.6411	0.0050	0.9916
K2PG	37	-760.9959	1731.2636	0.0036	0.9952
GTR	43	-744.2112	1731.6300	0.0030	0.9983
GTRI	44	-742.7322	1734.3280	0.0008	0.9991
GTRG	44	-743.0406	1734.9448	0.0006	0.9996
K2PIG	38	-760.6940	1736.3158	0.0003	0.9999
GTRIG	45	-742.7415	1740.0027	0.0000	1.0000
SYM	40	-758.9923	1744.2242	0.0000	1.0000
F81	38	-764.7741	1744.4759	0.0000	1.0000
SYMI	41	-757.6166	1747.1288	0.0000	1.0000
F81I	39	-763.4792	1747.5421	0.0000	1.0000
SYMG	41	-757.9561	1747.8079	0.0000	1.0000
F81G	39	-763.7496	1748.0830	0.0000	1.0000
JC69	35	-776.8263	1751.6123	0.0000	1.0000
SYMIG	42	-757.6271	1752.8058	0.0000	1.0000
F81IG	40	-763.4880	1753.2156	0.0000	1.0000
JC69I	36	-775.4613	1754.5383	0.0000	1.0000
JC69G	36	-775.7571	1755.1299	0.0000	1.0000
JC69IG	37	-775.4704	1760.2124	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/chr2_25984.phylip = 1 - 286;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25984.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 (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25984.phylip = 1 - 286;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25984.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 BIC model (HKY)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25984.phylip = 1 - 286;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25984.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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End of Output

