
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:09 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/chr9_7189.phylip" (19 taxa, 241 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
Minimum BIC  model: K2PG


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	-713.1160	1522.6319	0.2943	0.2943
HKYI	40	-713.3793	1523.1585	0.2261	0.5204
K2PG	37	-718.1952	1524.2426	0.1315	0.6519
K2PI	37	-718.4313	1524.7149	0.1039	0.7558
HKYIG	41	-713.0712	1525.4490	0.0719	0.8277
GTRG	44	-709.0578	1526.3197	0.0466	0.8743
GTRI	44	-709.1417	1526.4876	0.0428	0.9171
K2PIG	38	-718.1675	1527.0082	0.0330	0.9501
SYMG	41	-714.5593	1528.4252	0.0162	0.9663
SYMI	41	-714.6739	1528.6544	0.0145	0.9808
GTRIG	45	-709.0562	1529.3432	0.0103	0.9911
SYMIG	42	-714.5623	1531.3671	0.0037	0.9948
JC69G	36	-724.2014	1533.4617	0.0013	0.9961
F81G	39	-720.0746	1533.6716	0.0012	0.9973
JC69I	36	-724.4002	1533.8592	0.0011	0.9984
F81I	39	-720.2955	1534.1134	0.0009	0.9993
JC69IG	37	-724.1931	1536.2385	0.0003	0.9997
F81IG	40	-720.0577	1536.5155	0.0003	0.9999
HKY	39	-723.6710	1540.8643	0.0000	1.0000
K2P	36	-728.0919	1541.2427	0.0000	1.0000
SYM	40	-724.8939	1546.1879	0.0000	1.0000
GTR	43	-720.5911	1546.3904	0.0000	1.0000
JC69	35	-733.9714	1550.2355	0.0000	1.0000
F81	38	-730.1466	1550.9664	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-709.0578	1506.1156	0.2098	0.2098
HKYG	40	-713.1160	1506.2319	0.1979	0.4077
GTRI	44	-709.1417	1506.2835	0.1929	0.6005
HKYI	40	-713.3793	1506.7585	0.1521	0.7526
GTRIG	45	-709.0562	1508.1125	0.0773	0.8299
HKYIG	41	-713.0712	1508.1424	0.0761	0.9060
K2PG	37	-718.1952	1510.3904	0.0247	0.9308
K2PI	37	-718.4313	1510.8626	0.0195	0.9503
SYMG	41	-714.5593	1511.1186	0.0172	0.9675
SYMI	41	-714.6739	1511.3478	0.0153	0.9828
K2PIG	38	-718.1675	1512.3349	0.0094	0.9922
SYMIG	42	-714.5623	1513.1247	0.0063	0.9985
F81G	39	-720.0746	1518.1493	0.0005	0.9990
F81I	39	-720.2955	1518.5910	0.0004	0.9994
F81IG	40	-720.0577	1520.1155	0.0002	0.9996
JC69G	36	-724.2014	1520.4028	0.0002	0.9998
JC69I	36	-724.4002	1520.8004	0.0001	0.9999
JC69IG	37	-724.1931	1522.3863	0.0001	1.0000
HKY	39	-723.6710	1525.3420	0.0000	1.0000
GTR	43	-720.5911	1527.1823	0.0000	1.0000
K2P	36	-728.0919	1528.1839	0.0000	1.0000
SYM	40	-724.8939	1529.7879	0.0000	1.0000
F81	38	-730.1466	1536.2932	0.0000	1.0000
JC69	35	-733.9714	1537.9428	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-718.1952	1639.3278	0.4975	0.4975
K2PI	37	-718.4313	1639.8001	0.3928	0.8903
K2PIG	38	-718.1675	1644.7572	0.0329	0.9232
HKYG	40	-713.1160	1645.6238	0.0214	0.9446
JC69G	36	-724.2014	1645.8555	0.0190	0.9636
HKYI	40	-713.3793	1646.1504	0.0164	0.9801
JC69I	36	-724.4002	1646.2531	0.0156	0.9956
HKYIG	41	-713.0712	1651.0191	0.0014	0.9971
JC69IG	37	-724.1931	1651.3238	0.0012	0.9983
K2P	36	-728.0919	1653.6365	0.0004	0.9987
SYMG	41	-714.5593	1653.9953	0.0003	0.9990
F81G	39	-720.0746	1654.0563	0.0003	0.9993
SYMI	41	-714.6739	1654.2245	0.0003	0.9996
F81I	39	-720.2955	1654.4981	0.0003	0.9999
GTRG	44	-709.0578	1659.4466	0.0000	0.9999
SYMIG	42	-714.5623	1659.4862	0.0000	0.9999
F81IG	40	-720.0577	1659.5074	0.0000	1.0000
GTRI	44	-709.1417	1659.6145	0.0000	1.0000
JC69	35	-733.9714	1659.9107	0.0000	1.0000
HKY	39	-723.6710	1661.2490	0.0000	1.0000
GTRIG	45	-709.0562	1664.9283	0.0000	1.0000
F81	38	-730.1466	1668.7155	0.0000	1.0000
SYM	40	-724.8939	1669.1797	0.0000	1.0000
GTR	43	-720.5911	1677.0285	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/chr9_7189.phylip = 1 - 241;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_7189.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/chr9_7189.phylip = 1 - 241;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_7189.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_7189.phylip = 1 - 241;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_7189.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

