
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/chr5_11165.phylip" (19 taxa, 269 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	-634.3631	1363.1122	0.2881	0.2881
HKYI	40	-634.3691	1363.1243	0.2864	0.5745
GTRG	44	-629.6711	1365.0207	0.1110	0.6854
GTRI	44	-629.6764	1365.0313	0.1104	0.7958
HKYIG	41	-634.3628	1365.8974	0.0716	0.8674
GTRIG	45	-629.6707	1367.9064	0.0262	0.8936
HKY	39	-638.1415	1367.9075	0.0262	0.9198
K2PG	37	-641.1439	1368.4609	0.0199	0.9397
K2PI	37	-641.1656	1368.5044	0.0194	0.9591
SYMG	41	-636.2427	1369.6572	0.0109	0.9700
SYMI	41	-636.2638	1369.6994	0.0107	0.9807
GTR	43	-633.6093	1370.0364	0.0090	0.9898
K2PIG	38	-641.1441	1371.1752	0.0051	0.9949
SYMIG	42	-636.2442	1372.4708	0.0027	0.9975
K2P	36	-645.0347	1373.5522	0.0016	0.9991
SYM	40	-640.2719	1374.9299	0.0008	0.9999
F81G	39	-644.4990	1380.6225	0.0000	0.9999
F81I	39	-644.5123	1380.6491	0.0000	1.0000
F81IG	40	-644.5030	1383.3919	0.0000	1.0000
JC69G	36	-650.7062	1384.8951	0.0000	1.0000
JC69I	36	-650.7284	1384.9396	0.0000	1.0000
F81	38	-648.2568	1385.4006	0.0000	1.0000
JC69IG	37	-650.7057	1387.5846	0.0000	1.0000
JC69	35	-654.5502	1389.9158	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-629.6711	1347.3421	0.2685	0.2685
GTRI	44	-629.6764	1347.3527	0.2671	0.5356
HKYG	40	-634.3631	1348.7262	0.1344	0.6701
HKYI	40	-634.3691	1348.7383	0.1336	0.8037
GTRIG	45	-629.6707	1349.3414	0.0988	0.9025
HKYIG	41	-634.3628	1350.7256	0.0495	0.9520
GTR	43	-633.6093	1353.2186	0.0142	0.9662
HKY	39	-638.1415	1354.2830	0.0084	0.9745
SYMG	41	-636.2427	1354.4854	0.0075	0.9821
SYMI	41	-636.2638	1354.5276	0.0074	0.9895
K2PG	37	-641.1439	1356.2877	0.0031	0.9925
K2PI	37	-641.1656	1356.3313	0.0030	0.9955
SYMIG	42	-636.2442	1356.4885	0.0028	0.9983
K2PIG	38	-641.1441	1358.2882	0.0011	0.9994
SYM	40	-640.2719	1360.5439	0.0004	0.9998
K2P	36	-645.0347	1362.0695	0.0002	1.0000
F81G	39	-644.4990	1366.9981	0.0000	1.0000
F81I	39	-644.5123	1367.0246	0.0000	1.0000
F81IG	40	-644.5030	1369.0060	0.0000	1.0000
F81	38	-648.2568	1372.5137	0.0000	1.0000
JC69G	36	-650.7062	1373.4124	0.0000	1.0000
JC69I	36	-650.7284	1373.4568	0.0000	1.0000
JC69IG	37	-650.7057	1375.4114	0.0000	1.0000
JC69	35	-654.5502	1379.1004	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-641.1439	1489.2921	0.3487	0.3487
K2PI	37	-641.1656	1489.3356	0.3412	0.6899
K2P	36	-645.0347	1491.4791	0.1168	0.8068
HKYG	40	-634.3631	1492.5147	0.0696	0.8764
HKYI	40	-634.3691	1492.5268	0.0692	0.9456
HKY	39	-638.1415	1494.4767	0.0261	0.9717
K2PIG	38	-641.1441	1494.8873	0.0213	0.9929
HKYIG	41	-634.3628	1498.1088	0.0042	0.9972
SYMG	41	-636.2427	1501.8686	0.0006	0.9978
SYMI	41	-636.2638	1501.9107	0.0006	0.9985
JC69G	36	-650.7062	1502.8220	0.0004	0.9989
JC69I	36	-650.7284	1502.8664	0.0004	0.9992
SYM	40	-640.2719	1504.3324	0.0002	0.9994
JC69	35	-654.5502	1504.9153	0.0001	0.9996
GTRG	44	-629.6711	1505.5094	0.0001	0.9997
GTRI	44	-629.6764	1505.5200	0.0001	0.9998
F81G	39	-644.4990	1507.1918	0.0000	0.9998
F81I	39	-644.5123	1507.2183	0.0000	0.9999
SYMIG	42	-636.2442	1507.4663	0.0000	0.9999
GTR	43	-633.6093	1507.7912	0.0000	0.9999
JC69IG	37	-650.7057	1508.4158	0.0000	1.0000
F81	38	-648.2568	1509.1127	0.0000	1.0000
GTRIG	45	-629.6707	1511.1034	0.0000	1.0000
F81IG	40	-644.5030	1512.7944	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/chr5_11165.phylip = 1 - 269;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11165.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/chr5_11165.phylip = 1 - 269;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11165.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/chr5_11165.phylip = 1 - 269;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11165.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

