
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:20 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/chrZ_4832.phylip" (19 taxa, 209 characters)

Minimum AIC  model: GTRG
Minimum AICc model: K2P
Minimum BIC  model: K2P


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
K2P	36	-678.9603	1445.4089	0.3365	0.3365
K2PG	37	-678.0333	1446.5111	0.1939	0.5304
K2PI	37	-678.2177	1446.8797	0.1613	0.6916
HKY	39	-675.7230	1447.9075	0.0965	0.7881
HKYG	40	-674.6095	1448.7427	0.0635	0.8516
HKYI	40	-674.7436	1449.0110	0.0556	0.9072
K2PIG	38	-678.0329	1449.5011	0.0435	0.9507
HKYIG	41	-674.6241	1451.8710	0.0133	0.9640
GTRG	44	-670.2747	1452.6958	0.0088	0.9728
GTR	43	-671.8962	1452.7258	0.0087	0.9815
GTRI	44	-670.4402	1453.0267	0.0075	0.9889
SYM	40	-677.3334	1454.1906	0.0042	0.9931
SYMG	41	-676.2750	1455.1729	0.0026	0.9956
SYMI	41	-676.4665	1455.5559	0.0021	0.9977
GTRIG	45	-670.2766	1455.9519	0.0017	0.9995
SYMIG	42	-676.2745	1458.3080	0.0005	1.0000
JC69	35	-693.0453	1470.6571	0.0000	1.0000
JC69G	36	-692.4113	1472.3110	0.0000	1.0000
JC69I	36	-692.5358	1472.5599	0.0000	1.0000
F81	38	-689.7562	1472.9476	0.0000	1.0000
F81G	39	-689.1231	1474.7078	0.0000	1.0000
F81I	39	-689.2316	1474.9247	0.0000	1.0000
JC69IG	37	-692.4109	1475.2663	0.0000	1.0000
F81IG	40	-689.1228	1477.7693	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-670.2747	1428.5494	0.1497	0.1497
GTRI	44	-670.4402	1428.8804	0.1268	0.2765
HKYG	40	-674.6095	1429.2189	0.1071	0.3836
HKY	39	-675.7230	1429.4459	0.0956	0.4792
HKYI	40	-674.7436	1429.4872	0.0936	0.5729
GTR	43	-671.8962	1429.7925	0.0804	0.6533
K2P	36	-678.9603	1429.9206	0.0754	0.7287
K2PG	37	-678.0333	1430.0666	0.0701	0.7988
K2PI	37	-678.2177	1430.4353	0.0583	0.8570
GTRIG	45	-670.2766	1430.5532	0.0550	0.9120
HKYIG	41	-674.6241	1431.2482	0.0388	0.9508
K2PIG	38	-678.0329	1432.0658	0.0258	0.9766
SYMG	41	-676.2750	1434.5501	0.0074	0.9841
SYM	40	-677.3334	1434.6668	0.0070	0.9911
SYMI	41	-676.4665	1434.9331	0.0062	0.9973
SYMIG	42	-676.2745	1436.5490	0.0027	1.0000
F81	38	-689.7562	1455.5123	0.0000	1.0000
JC69	35	-693.0453	1456.0906	0.0000	1.0000
F81G	39	-689.1231	1456.2462	0.0000	1.0000
F81I	39	-689.2316	1456.4632	0.0000	1.0000
JC69G	36	-692.4113	1456.8226	0.0000	1.0000
JC69I	36	-692.5358	1457.0716	0.0000	1.0000
F81IG	40	-689.1228	1458.2455	0.0000	1.0000
JC69IG	37	-692.4109	1458.8219	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2P	36	-678.9603	1550.2446	0.7439	0.7439
K2PG	37	-678.0333	1553.7330	0.1300	0.8739
K2PI	37	-678.2177	1554.1017	0.1081	0.9820
K2PIG	38	-678.0329	1559.0745	0.0090	0.9910
HKY	39	-675.7230	1559.7970	0.0063	0.9973
HKYG	40	-674.6095	1562.9123	0.0013	0.9986
HKYI	40	-674.7436	1563.1806	0.0012	0.9998
HKYIG	41	-674.6241	1568.2839	0.0001	0.9999
SYM	40	-677.3334	1568.3602	0.0001	0.9999
SYMG	41	-676.2750	1571.5858	0.0000	1.0000
SYMI	41	-676.4665	1571.9688	0.0000	1.0000
JC69	35	-693.0453	1573.0723	0.0000	1.0000
GTR	43	-671.8962	1573.5129	0.0000	1.0000
GTRG	44	-670.2747	1575.6121	0.0000	1.0000
GTRI	44	-670.4402	1575.9431	0.0000	1.0000
SYMIG	42	-676.2745	1576.9270	0.0000	1.0000
JC69G	36	-692.4113	1577.1467	0.0000	1.0000
JC69I	36	-692.5358	1577.3956	0.0000	1.0000
GTRIG	45	-670.2766	1580.9582	0.0000	1.0000
JC69IG	37	-692.4109	1582.4882	0.0000	1.0000
F81	38	-689.7562	1582.5210	0.0000	1.0000
F81G	39	-689.1231	1586.5973	0.0000	1.0000
F81I	39	-689.2316	1586.8142	0.0000	1.0000
F81IG	40	-689.1228	1591.9389	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/chrZ_4832.phylip = 1 - 209;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4832.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 (K2P)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4832.phylip = 1 - 209;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4832.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0);
END;


[Mrbayes block for the best BIC model (K2P)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4832.phylip = 1 - 209;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4832.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0);
END;


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End of Output

