
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:56 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_21299.phylip" (19 taxa, 302 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
Minimum BIC  model: HKYG


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	-760.1560	1612.8790	0.6257	0.6257
HKYI	40	-761.1289	1614.8249	0.2365	0.8621
HKYIG	41	-760.7380	1616.7221	0.0916	0.9537
GTRG	44	-757.8472	1619.1030	0.0279	0.9816
GTRI	44	-758.8481	1621.1048	0.0102	0.9918
GTRIG	45	-758.4691	1623.1101	0.0038	0.9956
HKY	39	-766.6354	1623.1792	0.0036	0.9992
K2PG	37	-771.5023	1627.6560	0.0004	0.9996
K2PI	37	-772.2460	1629.1435	0.0002	0.9998
GTR	43	-764.9080	1630.4827	0.0001	0.9999
K2PIG	38	-771.9186	1631.1072	0.0001	0.9999
SYMG	41	-769.0330	1633.3121	0.0000	1.0000
F81G	39	-772.3369	1634.5822	0.0000	1.0000
SYMI	41	-769.8744	1634.9950	0.0000	1.0000
F81I	39	-772.6720	1635.2525	0.0000	1.0000
K2P	36	-777.4539	1636.9606	0.0000	1.0000
SYMIG	42	-769.5767	1637.0993	0.0000	1.0000
F81IG	40	-772.3410	1637.2491	0.0000	1.0000
F81	38	-777.8827	1643.0353	0.0000	1.0000
SYM	40	-775.3533	1643.2736	0.0000	1.0000
JC69G	36	-784.0251	1650.1030	0.0000	1.0000
JC69I	36	-784.3005	1650.6538	0.0000	1.0000
JC69IG	37	-783.9804	1652.6123	0.0000	1.0000
JC69	35	-789.2716	1658.0169	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-760.1560	1600.3120	0.5327	0.5327
HKYI	40	-761.1289	1602.2578	0.2014	0.7341
HKYIG	41	-760.7380	1603.4760	0.1095	0.8436
GTRG	44	-757.8472	1603.6944	0.0982	0.9418
GTRI	44	-758.8481	1605.6962	0.0361	0.9779
GTRIG	45	-758.4691	1606.9382	0.0194	0.9973
HKY	39	-766.6354	1611.2708	0.0022	0.9995
GTR	43	-764.9080	1615.8160	0.0002	0.9997
K2PG	37	-771.5023	1617.0045	0.0001	0.9998
K2PI	37	-772.2460	1618.4919	0.0001	0.9999
K2PIG	38	-771.9186	1619.8372	0.0000	0.9999
SYMG	41	-769.0330	1620.0660	0.0000	1.0000
SYMI	41	-769.8744	1621.7488	0.0000	1.0000
F81G	39	-772.3369	1622.6738	0.0000	1.0000
SYMIG	42	-769.5767	1623.1533	0.0000	1.0000
F81I	39	-772.6720	1623.3441	0.0000	1.0000
F81IG	40	-772.3410	1624.6820	0.0000	1.0000
K2P	36	-777.4539	1626.9078	0.0000	1.0000
SYM	40	-775.3533	1630.7065	0.0000	1.0000
F81	38	-777.8827	1631.7653	0.0000	1.0000
JC69G	36	-784.0251	1640.0502	0.0000	1.0000
JC69I	36	-784.3005	1640.6010	0.0000	1.0000
JC69IG	37	-783.9804	1641.9608	0.0000	1.0000
JC69	35	-789.2716	1648.5432	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-760.1560	1748.7291	0.6520	0.6520
HKYI	40	-761.1289	1750.6749	0.2464	0.8984
K2PG	37	-771.5023	1754.2903	0.0404	0.9388
HKYIG	41	-760.7380	1755.6035	0.0210	0.9598
K2PI	37	-772.2460	1755.7777	0.0192	0.9790
HKY	39	-766.6354	1755.9774	0.0174	0.9964
K2P	36	-777.4539	1760.4832	0.0018	0.9982
K2PIG	38	-771.9186	1760.8335	0.0015	0.9998
GTRG	44	-757.8472	1766.9532	0.0001	0.9999
F81G	39	-772.3369	1767.3804	0.0001	0.9999
F81I	39	-772.6720	1768.0507	0.0000	1.0000
GTRI	44	-758.8481	1768.9550	0.0000	1.0000
SYMG	41	-769.0330	1772.1935	0.0000	1.0000
F81	38	-777.8827	1772.7615	0.0000	1.0000
F81IG	40	-772.3410	1773.0991	0.0000	1.0000
JC69G	36	-784.0251	1773.6256	0.0000	1.0000
SYMI	41	-769.8744	1773.8763	0.0000	1.0000
GTRIG	45	-758.4691	1773.9074	0.0000	1.0000
JC69I	36	-784.3005	1774.1764	0.0000	1.0000
GTR	43	-764.9080	1775.3644	0.0000	1.0000
JC69	35	-789.2716	1778.4082	0.0000	1.0000
SYMIG	42	-769.5767	1778.9913	0.0000	1.0000
SYM	40	-775.3533	1779.1236	0.0000	1.0000
JC69IG	37	-783.9804	1779.2466	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21299.phylip = 1 - 302;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21299.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 AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21299.phylip = 1 - 302;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21299.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21299.phylip = 1 - 302;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21299.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;


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End of Output

