
Output from mraic.pl version 1.4.4 by Johan Nylander
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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_7907.phylip" (19 taxa, 234 characters)

Minimum AIC  model: HKYI
Minimum AICc model: K2PG
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
K2PG	37	-649.8829	1388.1128	0.2909	0.2909
K2PI	37	-649.9005	1388.1480	0.2858	0.5767
HKYI	40	-646.4719	1389.9386	0.1168	0.6935
HKYG	40	-646.5574	1390.1096	0.1072	0.8007
K2PIG	38	-649.8939	1390.9879	0.0691	0.8698
K2P	36	-653.2196	1391.9620	0.0425	0.9122
HKY	39	-649.4618	1393.0062	0.0252	0.9374
HKYIG	41	-646.5603	1393.0581	0.0245	0.9620
SYMG	41	-647.4793	1394.8960	0.0098	0.9718
SYMI	41	-647.5595	1395.0565	0.0090	0.9808
GTRG	44	-643.4374	1395.8272	0.0061	0.9869
GTRI	44	-643.4653	1395.8831	0.0060	0.9929
SYMIG	42	-647.4897	1397.8904	0.0022	0.9951
SYM	40	-650.6423	1398.2795	0.0018	0.9969
GTR	43	-646.2136	1398.3430	0.0017	0.9987
GTRIG	45	-643.4398	1398.9009	0.0013	1.0000
JC69I	36	-661.7329	1408.9887	0.0000	1.0000
JC69G	36	-661.8201	1409.1630	0.0000	1.0000
F81I	39	-658.6254	1411.3332	0.0000	1.0000
JC69	35	-664.3664	1411.4602	0.0000	1.0000
F81G	39	-658.7297	1411.5419	0.0000	1.0000
JC69IG	37	-661.8216	1411.9901	0.0000	1.0000
F81	38	-661.1476	1413.4951	0.0000	1.0000
F81IG	40	-658.6278	1414.2505	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-646.4719	1372.9438	0.1891	0.1891
HKYG	40	-646.5574	1373.1148	0.1736	0.3626
K2PG	37	-649.8829	1373.7658	0.1253	0.4880
K2PI	37	-649.9005	1373.8010	0.1232	0.6111
GTRG	44	-643.4374	1374.8748	0.0720	0.6831
GTRI	44	-643.4653	1374.9307	0.0700	0.7531
HKYIG	41	-646.5603	1375.1206	0.0637	0.8168
K2PIG	38	-649.8939	1375.7879	0.0456	0.8624
GTRIG	45	-643.4398	1376.8796	0.0264	0.8888
HKY	39	-649.4618	1376.9237	0.0258	0.9147
SYMG	41	-647.4793	1376.9585	0.0254	0.9401
SYMI	41	-647.5595	1377.1190	0.0234	0.9635
GTR	43	-646.2136	1378.4272	0.0122	0.9757
K2P	36	-653.2196	1378.4391	0.0121	0.9878
SYMIG	42	-647.4897	1378.9794	0.0092	0.9971
SYM	40	-650.6423	1381.2847	0.0029	1.0000
F81I	39	-658.6254	1395.2508	0.0000	1.0000
F81G	39	-658.7297	1395.4594	0.0000	1.0000
JC69I	36	-661.7329	1395.4659	0.0000	1.0000
JC69G	36	-661.8201	1395.6402	0.0000	1.0000
F81IG	40	-658.6278	1397.2557	0.0000	1.0000
JC69IG	37	-661.8216	1397.6432	0.0000	1.0000
F81	38	-661.1476	1398.2951	0.0000	1.0000
JC69	35	-664.3664	1398.7329	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-649.8829	1501.6127	0.3824	0.3824
K2PI	37	-649.9005	1501.6479	0.3757	0.7581
K2P	36	-653.2196	1502.8307	0.2080	0.9660
K2PIG	38	-649.8939	1507.0901	0.0247	0.9908
HKYI	40	-646.4719	1511.1567	0.0032	0.9940
HKYG	40	-646.5574	1511.3276	0.0030	0.9970
HKY	39	-649.4618	1511.6812	0.0025	0.9995
HKYIG	41	-646.5603	1516.7888	0.0002	0.9997
SYMG	41	-647.4793	1518.6267	0.0001	0.9997
SYMI	41	-647.5595	1518.7872	0.0001	0.9998
SYM	40	-650.6423	1519.4975	0.0000	0.9999
JC69	35	-664.3664	1519.6691	0.0000	0.9999
JC69I	36	-661.7329	1519.8574	0.0000	0.9999
JC69G	36	-661.8201	1520.0317	0.0000	1.0000
SYMIG	42	-647.4897	1524.1029	0.0000	1.0000
JC69IG	37	-661.8216	1525.4901	0.0000	1.0000
GTRG	44	-643.4374	1526.9089	0.0000	1.0000
GTRI	44	-643.4653	1526.9648	0.0000	1.0000
GTR	43	-646.2136	1527.0060	0.0000	1.0000
F81	38	-661.1476	1529.5973	0.0000	1.0000
F81I	39	-658.6254	1530.0083	0.0000	1.0000
F81G	39	-658.7297	1530.2169	0.0000	1.0000
GTRIG	45	-643.4398	1532.3691	0.0000	1.0000
F81IG	40	-658.6278	1535.4685	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/chr2_7907.phylip = 1 - 234;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7907.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7907.phylip = 1 - 234;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7907.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;


[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/chr2_7907.phylip = 1 - 234;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7907.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

