
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:54 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/chr7_1665.phylip" (19 taxa, 227 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: HKYI


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
HKYI	40	-627.0227	1351.6799	0.4584	0.4584
HKYG	40	-627.0972	1351.8288	0.4255	0.8839
HKYIG	41	-627.0971	1354.8105	0.0958	0.9797
GTRI	44	-624.8425	1359.4432	0.0095	0.9891
GTRG	44	-624.9596	1359.6773	0.0084	0.9975
GTRIG	45	-624.9595	1362.7919	0.0018	0.9993
F81I	39	-635.7600	1366.2045	0.0003	0.9996
F81G	39	-635.8552	1366.3949	0.0003	0.9999
F81IG	40	-635.8551	1369.3446	0.0001	1.0000
K2PI	37	-643.1806	1375.2395	0.0000	1.0000
K2PG	37	-643.2787	1375.4357	0.0000	1.0000
HKY	39	-640.3979	1375.4802	0.0000	1.0000
K2PIG	38	-643.2787	1378.3233	0.0000	1.0000
SYMI	41	-641.3646	1383.3453	0.0000	1.0000
GTR	43	-638.4173	1383.5122	0.0000	1.0000
SYMG	41	-641.4699	1383.5560	0.0000	1.0000
SYMIG	42	-641.4699	1386.5702	0.0000	1.0000
F81	38	-648.9892	1389.7444	0.0000	1.0000
JC69I	36	-654.7804	1395.5820	0.0000	1.0000
JC69G	36	-654.8872	1395.7955	0.0000	1.0000
JC69IG	37	-654.8872	1398.6527	0.0000	1.0000
K2P	36	-656.7347	1399.4905	0.0000	1.0000
SYM	40	-655.1902	1408.0147	0.0000	1.0000
JC69	35	-668.0347	1419.2631	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-627.0227	1334.0455	0.3802	0.3802
HKYG	40	-627.0972	1334.1944	0.3529	0.7332
HKYIG	41	-627.0971	1336.1943	0.1298	0.8630
GTRI	44	-624.8425	1337.6850	0.0616	0.9246
GTRG	44	-624.9596	1337.9191	0.0548	0.9795
GTRIG	45	-624.9595	1339.9190	0.0202	0.9996
F81I	39	-635.7600	1349.5200	0.0002	0.9998
F81G	39	-635.8552	1349.7104	0.0002	0.9999
F81IG	40	-635.8551	1351.7102	0.0001	1.0000
HKY	39	-640.3979	1358.7957	0.0000	1.0000
K2PI	37	-643.1806	1360.3612	0.0000	1.0000
K2PG	37	-643.2787	1360.5574	0.0000	1.0000
K2PIG	38	-643.2787	1362.5573	0.0000	1.0000
GTR	43	-638.4173	1362.8346	0.0000	1.0000
SYMI	41	-641.3646	1364.7291	0.0000	1.0000
SYMG	41	-641.4699	1364.9398	0.0000	1.0000
SYMIG	42	-641.4699	1366.9397	0.0000	1.0000
F81	38	-648.9892	1373.9784	0.0000	1.0000
JC69I	36	-654.7804	1381.5609	0.0000	1.0000
JC69G	36	-654.8872	1381.7745	0.0000	1.0000
JC69IG	37	-654.8872	1383.7744	0.0000	1.0000
K2P	36	-656.7347	1385.4695	0.0000	1.0000
SYM	40	-655.1902	1390.3803	0.0000	1.0000
JC69	35	-668.0347	1406.0694	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-627.0227	1471.0435	0.5011	0.5011
HKYG	40	-627.0972	1471.1924	0.4651	0.9662
HKYIG	41	-627.0971	1476.6172	0.0309	0.9971
F81I	39	-635.7600	1483.0931	0.0012	0.9983
F81G	39	-635.8552	1483.2834	0.0011	0.9994
K2PI	37	-643.1806	1487.0843	0.0002	0.9996
K2PG	37	-643.2787	1487.2806	0.0001	0.9997
GTRI	44	-624.8425	1488.3828	0.0001	0.9998
GTRG	44	-624.9596	1488.6169	0.0001	0.9999
F81IG	40	-635.8551	1488.7082	0.0001	1.0000
HKY	39	-640.3979	1492.3688	0.0000	1.0000
K2PIG	38	-643.2787	1492.7054	0.0000	1.0000
GTRIG	45	-624.9595	1494.0418	0.0000	1.0000
F81	38	-648.9892	1504.1265	0.0000	1.0000
JC69I	36	-654.7804	1504.8591	0.0000	1.0000
JC69G	36	-654.8872	1505.0727	0.0000	1.0000
SYMI	41	-641.3646	1505.1521	0.0000	1.0000
SYMG	41	-641.4699	1505.3627	0.0000	1.0000
K2P	36	-656.7347	1508.7677	0.0000	1.0000
GTR	43	-638.4173	1510.1074	0.0000	1.0000
JC69IG	37	-654.8872	1510.4976	0.0000	1.0000
SYMIG	42	-641.4699	1510.7876	0.0000	1.0000
JC69	35	-668.0347	1525.9427	0.0000	1.0000
SYM	40	-655.1902	1527.3783	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1665.phylip = 1 - 227;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1665.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1665.phylip = 1 - 227;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1665.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1665.phylip = 1 - 227;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1665.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

