
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:06 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/chr8_3445.phylip" (19 taxa, 267 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	-740.9825	1576.4782	0.3404	0.3404
HKYI	40	-741.1437	1576.8006	0.2897	0.6301
GTRG	44	-736.1805	1578.1989	0.1440	0.7741
GTRI	44	-736.4829	1578.8036	0.1064	0.8805
HKYIG	41	-740.9810	1579.2687	0.0843	0.9648
GTRIG	45	-736.1805	1581.0940	0.0339	0.9987
K2PG	37	-751.5832	1589.4458	0.0005	0.9992
K2PI	37	-751.8484	1589.9762	0.0004	0.9996
GTR	43	-744.4016	1591.7717	0.0002	0.9997
K2PIG	38	-751.5414	1592.0828	0.0001	0.9999
HKY	39	-751.2987	1594.3420	0.0000	0.9999
SYMG	41	-748.6539	1594.6144	0.0000	1.0000
SYMI	41	-748.9135	1595.1336	0.0000	1.0000
SYMIG	42	-748.6336	1597.3923	0.0000	1.0000
F81G	39	-756.1860	1604.1164	0.0000	1.0000
F81I	39	-756.4476	1604.6397	0.0000	1.0000
F81IG	40	-756.1647	1606.8427	0.0000	1.0000
K2P	36	-762.5149	1608.6124	0.0000	1.0000
SYM	40	-758.2792	1611.0717	0.0000	1.0000
JC69G	36	-765.8008	1615.1842	0.0000	1.0000
JC69I	36	-766.1040	1615.7905	0.0000	1.0000
JC69IG	37	-765.7462	1617.7720	0.0000	1.0000
F81	38	-765.8642	1620.7284	0.0000	1.0000
JC69	35	-776.1029	1633.1150	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-736.1805	1560.3611	0.3222	0.3222
GTRI	44	-736.4829	1560.9658	0.2381	0.5603
HKYG	40	-740.9825	1561.9649	0.1445	0.7048
HKYI	40	-741.1437	1562.2873	0.1230	0.8278
GTRIG	45	-736.1805	1562.3610	0.1185	0.9463
HKYIG	41	-740.9810	1563.9620	0.0532	0.9995
GTR	43	-744.4016	1574.8031	0.0002	0.9998
K2PG	37	-751.5832	1577.1663	0.0001	0.9999
K2PI	37	-751.8484	1577.6967	0.0001	0.9999
K2PIG	38	-751.5414	1579.0828	0.0000	0.9999
SYMG	41	-748.6539	1579.3077	0.0000	1.0000
SYMI	41	-748.9135	1579.8269	0.0000	1.0000
HKY	39	-751.2987	1580.5975	0.0000	1.0000
SYMIG	42	-748.6336	1581.2673	0.0000	1.0000
F81G	39	-756.1860	1590.3719	0.0000	1.0000
F81I	39	-756.4476	1590.8952	0.0000	1.0000
F81IG	40	-756.1647	1592.3294	0.0000	1.0000
SYM	40	-758.2792	1596.5584	0.0000	1.0000
K2P	36	-762.5149	1597.0298	0.0000	1.0000
JC69G	36	-765.8008	1603.6016	0.0000	1.0000
JC69I	36	-766.1040	1604.2079	0.0000	1.0000
JC69IG	37	-765.7462	1605.4925	0.0000	1.0000
F81	38	-765.8642	1607.7284	0.0000	1.0000
JC69	35	-776.1029	1622.2059	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-740.9825	1705.4549	0.4728	0.4728
HKYI	40	-741.1437	1705.7773	0.4024	0.8752
K2PG	37	-751.5832	1709.8945	0.0514	0.9266
K2PI	37	-751.8484	1710.4249	0.0394	0.9660
HKYIG	41	-740.9810	1711.0392	0.0290	0.9950
K2PIG	38	-751.5414	1715.3982	0.0033	0.9982
GTRG	44	-736.1805	1718.2000	0.0008	0.9991
GTRI	44	-736.4829	1718.8047	0.0006	0.9996
HKY	39	-751.2987	1720.5002	0.0003	0.9999
GTRIG	45	-736.1805	1723.7872	0.0000	1.0000
K2P	36	-762.5149	1726.1707	0.0000	1.0000
SYMG	41	-748.6539	1726.3849	0.0000	1.0000
SYMI	41	-748.9135	1726.9041	0.0000	1.0000
GTR	43	-744.4016	1729.0548	0.0000	1.0000
F81G	39	-756.1860	1730.2746	0.0000	1.0000
F81I	39	-756.4476	1730.7979	0.0000	1.0000
SYMIG	42	-748.6336	1731.9317	0.0000	1.0000
JC69G	36	-765.8008	1732.7425	0.0000	1.0000
JC69I	36	-766.1040	1733.3489	0.0000	1.0000
F81IG	40	-756.1647	1735.8193	0.0000	1.0000
JC69IG	37	-765.7462	1738.2207	0.0000	1.0000
SYM	40	-758.2792	1740.0483	0.0000	1.0000
F81	38	-765.8642	1744.0438	0.0000	1.0000
JC69	35	-776.1029	1747.7596	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/chr8_3445.phylip = 1 - 267;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_3445.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/chr8_3445.phylip = 1 - 267;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_3445.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/chr8_3445.phylip = 1 - 267;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_3445.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

