
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:32 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/chr9_393.phylip" (19 taxa, 232 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	-687.3059	1471.7845	0.4003	0.4003
HKYI	40	-687.9204	1473.0136	0.2165	0.6169
HKYIG	41	-687.1564	1474.4391	0.1062	0.7230
GTRG	44	-682.7223	1474.6210	0.0969	0.8200
GTRI	44	-683.2358	1475.6480	0.0580	0.8780
K2PG	37	-693.8948	1476.2845	0.0422	0.9202
K2PI	37	-694.3893	1477.2734	0.0257	0.9459
GTRIG	45	-682.6155	1477.4890	0.0231	0.9690
K2PIG	38	-693.7717	1478.9009	0.0114	0.9804
SYMG	41	-689.5524	1479.2312	0.0097	0.9901
SYMI	41	-689.9145	1479.9552	0.0067	0.9968
SYMIG	42	-689.4855	1482.0821	0.0023	0.9991
HKY	39	-695.2902	1484.8304	0.0006	0.9997
GTR	43	-690.7024	1487.5325	0.0002	0.9999
K2P	36	-701.4326	1488.5267	0.0001	1.0000
SYM	40	-697.0051	1491.1829	0.0000	1.0000
F81G	39	-700.1262	1494.5024	0.0000	1.0000
F81I	39	-700.5719	1495.3937	0.0000	1.0000
JC69G	36	-705.6367	1496.9349	0.0000	1.0000
F81IG	40	-700.0527	1497.2782	0.0000	1.0000
JC69I	36	-706.0188	1497.6992	0.0000	1.0000
JC69IG	37	-705.5708	1499.6364	0.0000	1.0000
F81	38	-707.2611	1505.8797	0.0000	1.0000
JC69	35	-712.6633	1508.1837	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-682.7223	1453.4446	0.3141	0.3141
GTRI	44	-683.2358	1454.4716	0.1879	0.5020
HKYG	40	-687.3059	1454.6118	0.1752	0.6773
GTRIG	45	-682.6155	1455.2309	0.1286	0.8058
HKYI	40	-687.9204	1455.8408	0.0948	0.9006
HKYIG	41	-687.1564	1456.3128	0.0749	0.9755
SYMG	41	-689.5524	1461.1049	0.0068	0.9823
K2PG	37	-693.8948	1461.7897	0.0048	0.9871
SYMI	41	-689.9145	1461.8289	0.0047	0.9919
K2PI	37	-694.3893	1462.7786	0.0030	0.9948
SYMIG	42	-689.4855	1462.9710	0.0027	0.9975
K2PIG	38	-693.7717	1463.5433	0.0020	0.9995
GTR	43	-690.7024	1467.4048	0.0003	0.9998
HKY	39	-695.2902	1468.5804	0.0002	1.0000
SYM	40	-697.0051	1474.0102	0.0000	1.0000
K2P	36	-701.4326	1474.8651	0.0000	1.0000
F81G	39	-700.1262	1478.2524	0.0000	1.0000
F81I	39	-700.5719	1479.1437	0.0000	1.0000
F81IG	40	-700.0527	1480.1054	0.0000	1.0000
JC69G	36	-705.6367	1483.2733	0.0000	1.0000
JC69I	36	-706.0188	1484.0377	0.0000	1.0000
JC69IG	37	-705.5708	1485.1415	0.0000	1.0000
F81	38	-707.2611	1490.5222	0.0000	1.0000
JC69	35	-712.6633	1495.3265	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-693.8948	1589.3189	0.4927	0.4927
K2PI	37	-694.3893	1590.3079	0.3005	0.7933
HKYG	40	-687.3059	1592.4813	0.1014	0.8947
HKYI	40	-687.9204	1593.7103	0.0548	0.9495
K2PIG	38	-693.7717	1594.5194	0.0366	0.9861
HKYIG	41	-687.1564	1597.6290	0.0077	0.9938
K2P	36	-701.4326	1598.9477	0.0040	0.9978
SYMG	41	-689.5524	1602.4211	0.0007	0.9985
HKY	39	-695.2902	1603.0032	0.0005	0.9990
SYMI	41	-689.9145	1603.1452	0.0005	0.9995
GTRG	44	-682.7223	1605.1010	0.0002	0.9997
GTRI	44	-683.2358	1606.1280	0.0001	0.9998
JC69G	36	-705.6367	1607.3559	0.0001	0.9999
SYMIG	42	-689.4855	1607.7339	0.0000	0.9999
JC69I	36	-706.0188	1608.1202	0.0000	1.0000
GTRIG	45	-682.6155	1610.3341	0.0000	1.0000
SYM	40	-697.0051	1611.8797	0.0000	1.0000
JC69IG	37	-705.5708	1612.6708	0.0000	1.0000
F81G	39	-700.1262	1612.6751	0.0000	1.0000
F81I	39	-700.5719	1613.5665	0.0000	1.0000
GTR	43	-690.7024	1615.6145	0.0000	1.0000
JC69	35	-712.6633	1615.9623	0.0000	1.0000
F81IG	40	-700.0527	1617.9749	0.0000	1.0000
F81	38	-707.2611	1621.4982	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/chr9_393.phylip = 1 - 232;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_393.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/chr9_393.phylip = 1 - 232;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_393.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/chr9_393.phylip = 1 - 232;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_393.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

