
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:19 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/chr1_32393.phylip" (19 taxa, 232 characters)

Minimum AIC  model: HKY
Minimum AICc model: HKY
Minimum BIC  model: HKY


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
HKY	39	-657.7553	1409.7605	0.5297	0.5297
HKYG	40	-657.2991	1411.7711	0.1938	0.7235
HKYI	40	-657.3324	1411.8376	0.1875	0.9110
HKYIG	41	-657.3054	1414.7372	0.0440	0.9550
GTR	43	-654.8038	1415.7353	0.0267	0.9817
GTRG	44	-654.4264	1418.0292	0.0085	0.9902
GTRI	44	-654.4970	1418.1705	0.0079	0.9981
GTRIG	45	-654.4343	1421.1266	0.0018	0.9999
F81	38	-668.7764	1428.9103	0.0000	1.0000
F81G	39	-668.1947	1430.6394	0.0000	1.0000
F81I	39	-668.2288	1430.7076	0.0000	1.0000
K2P	36	-673.6499	1432.9613	0.0000	1.0000
F81IG	40	-668.1998	1433.5723	0.0000	1.0000
K2PG	37	-672.9750	1434.4449	0.0000	1.0000
K2PI	37	-672.9801	1434.4550	0.0000	1.0000
K2PIG	38	-672.9737	1437.3050	0.0000	1.0000
SYM	40	-671.5483	1440.2694	0.0000	1.0000
SYMG	41	-670.9558	1442.0380	0.0000	1.0000
SYMI	41	-670.9643	1442.0549	0.0000	1.0000
SYMIG	42	-670.9553	1445.0217	0.0000	1.0000
JC69	35	-684.5512	1451.9595	0.0000	1.0000
JC69G	36	-683.8624	1453.3863	0.0000	1.0000
JC69I	36	-683.8710	1453.4035	0.0000	1.0000
JC69IG	37	-683.8616	1456.2181	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKY	39	-657.7553	1393.5105	0.3188	0.3188
HKYG	40	-657.2991	1394.5983	0.1851	0.5039
HKYI	40	-657.3324	1394.6649	0.1790	0.6829
GTR	43	-654.8038	1395.6077	0.1117	0.7946
HKYIG	41	-657.3054	1396.6109	0.0677	0.8623
GTRG	44	-654.4264	1396.8527	0.0599	0.9222
GTRI	44	-654.4970	1396.9940	0.0559	0.9781
GTRIG	45	-654.4343	1398.8686	0.0219	1.0000
F81	38	-668.7764	1413.5528	0.0000	1.0000
F81G	39	-668.1947	1414.3894	0.0000	1.0000
F81I	39	-668.2288	1414.4576	0.0000	1.0000
F81IG	40	-668.1998	1416.3996	0.0000	1.0000
K2P	36	-673.6499	1419.2998	0.0000	1.0000
K2PG	37	-672.9750	1419.9501	0.0000	1.0000
K2PI	37	-672.9801	1419.9602	0.0000	1.0000
K2PIG	38	-672.9737	1421.9475	0.0000	1.0000
SYM	40	-671.5483	1423.0966	0.0000	1.0000
SYMG	41	-670.9558	1423.9117	0.0000	1.0000
SYMI	41	-670.9643	1423.9285	0.0000	1.0000
SYMIG	42	-670.9553	1425.9106	0.0000	1.0000
JC69	35	-684.5512	1439.1024	0.0000	1.0000
JC69G	36	-683.8624	1439.7247	0.0000	1.0000
JC69I	36	-683.8710	1439.7419	0.0000	1.0000
JC69IG	37	-683.8616	1441.7232	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKY	39	-657.7553	1527.9333	0.8252	0.8252
HKYG	40	-657.2991	1532.4678	0.0855	0.9107
HKYI	40	-657.3324	1532.5344	0.0827	0.9934
HKYIG	41	-657.3054	1537.9271	0.0056	0.9989
K2P	36	-673.6499	1543.3823	0.0004	0.9993
GTR	43	-654.8038	1543.8174	0.0003	0.9996
F81	38	-668.7764	1544.5288	0.0002	0.9998
K2PG	37	-672.9750	1547.4793	0.0000	0.9998
K2PI	37	-672.9801	1547.4895	0.0000	0.9999
GTRG	44	-654.4264	1548.5092	0.0000	0.9999
GTRI	44	-654.4970	1548.6505	0.0000	0.9999
F81G	39	-668.1947	1548.8122	0.0000	1.0000
F81I	39	-668.2288	1548.8804	0.0000	1.0000
K2PIG	38	-672.9737	1552.9235	0.0000	1.0000
GTRIG	45	-654.4343	1553.9717	0.0000	1.0000
F81IG	40	-668.1998	1554.2691	0.0000	1.0000
JC69	35	-684.5512	1559.7382	0.0000	1.0000
SYM	40	-671.5483	1560.9661	0.0000	1.0000
JC69G	36	-683.8624	1563.8073	0.0000	1.0000
JC69I	36	-683.8710	1563.8245	0.0000	1.0000
SYMG	41	-670.9558	1565.2279	0.0000	1.0000
SYMI	41	-670.9643	1565.2448	0.0000	1.0000
JC69IG	37	-683.8616	1569.2525	0.0000	1.0000
SYMIG	42	-670.9553	1570.6736	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32393.phylip = 1 - 232;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32393.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32393.phylip = 1 - 232;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32393.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32393.phylip = 1 - 232;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32393.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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End of Output

