
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:06 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_3148.phylip" (19 taxa, 269 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-692.1724	1490.0234	0.4937	0.4937
GTRI	44	-692.6525	1490.9836	0.3055	0.7992
GTRIG	45	-692.1015	1492.7681	0.1252	0.9244
HKYG	40	-700.7773	1495.9405	0.0256	0.9500
HKYI	40	-700.9648	1496.3156	0.0212	0.9713
GTR	43	-696.7692	1496.3562	0.0208	0.9921
HKYIG	41	-700.7204	1498.6125	0.0067	0.9988
HKY	39	-705.2766	1502.1776	0.0011	0.9999
SYMG	41	-706.7756	1510.7230	0.0000	1.0000
SYMI	41	-706.9989	1511.1696	0.0000	1.0000
K2PG	37	-713.0506	1512.2744	0.0000	1.0000
K2PI	37	-713.1065	1512.3862	0.0000	1.0000
SYMIG	42	-706.7313	1513.4449	0.0000	1.0000
F81G	39	-711.4877	1514.5998	0.0000	1.0000
K2PIG	38	-712.9121	1514.7112	0.0000	1.0000
F81I	39	-711.6648	1514.9541	0.0000	1.0000
SYM	40	-711.3684	1517.1228	0.0000	1.0000
F81IG	40	-711.4450	1517.2759	0.0000	1.0000
K2P	36	-718.0581	1519.5991	0.0000	1.0000
F81	38	-715.9886	1520.8642	0.0000	1.0000
JC69G	36	-722.8455	1529.1738	0.0000	1.0000
JC69I	36	-722.9682	1529.4191	0.0000	1.0000
JC69IG	37	-722.8105	1531.7942	0.0000	1.0000
JC69	35	-726.2174	1533.2503	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-692.1724	1472.3448	0.4846	0.4846
GTRI	44	-692.6525	1473.3050	0.2998	0.7844
GTRIG	45	-692.1015	1474.2031	0.1914	0.9758
GTR	43	-696.7692	1479.5384	0.0133	0.9891
HKYG	40	-700.7773	1481.5545	0.0048	0.9939
HKYI	40	-700.9648	1481.9296	0.0040	0.9980
HKYIG	41	-700.7204	1483.4407	0.0019	0.9998
HKY	39	-705.2766	1488.5531	0.0001	1.0000
SYMG	41	-706.7756	1495.5512	0.0000	1.0000
SYMI	41	-706.9989	1495.9978	0.0000	1.0000
SYMIG	42	-706.7313	1497.4626	0.0000	1.0000
K2PG	37	-713.0506	1500.1012	0.0000	1.0000
K2PI	37	-713.1065	1500.2130	0.0000	1.0000
F81G	39	-711.4877	1500.9754	0.0000	1.0000
F81I	39	-711.6648	1501.3296	0.0000	1.0000
K2PIG	38	-712.9121	1501.8242	0.0000	1.0000
SYM	40	-711.3684	1502.7369	0.0000	1.0000
F81IG	40	-711.4450	1502.8900	0.0000	1.0000
F81	38	-715.9886	1507.9772	0.0000	1.0000
K2P	36	-718.0581	1508.1163	0.0000	1.0000
JC69G	36	-722.8455	1517.6911	0.0000	1.0000
JC69I	36	-722.9682	1517.9363	0.0000	1.0000
JC69IG	37	-722.8105	1519.6211	0.0000	1.0000
JC69	35	-726.2174	1522.4348	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-700.7773	1625.3430	0.4424	0.4424
HKYI	40	-700.9648	1625.7181	0.3668	0.8092
HKY	39	-705.2766	1628.7469	0.0807	0.8898
GTRG	44	-692.1724	1630.5121	0.0334	0.9232
HKYIG	41	-700.7204	1630.8239	0.0286	0.9518
GTRI	44	-692.6525	1631.4723	0.0206	0.9724
K2PG	37	-713.0506	1633.1055	0.0091	0.9815
K2PI	37	-713.1065	1633.2173	0.0086	0.9902
GTR	43	-696.7692	1634.1110	0.0055	0.9957
GTRIG	45	-692.1015	1635.9651	0.0022	0.9979
K2P	36	-718.0581	1637.5259	0.0010	0.9989
K2PIG	38	-712.9121	1638.4232	0.0006	0.9995
F81G	39	-711.4877	1641.1691	0.0002	0.9997
F81I	39	-711.6648	1641.5233	0.0001	0.9998
SYMG	41	-706.7756	1642.9344	0.0001	0.9999
SYMI	41	-706.9989	1643.3810	0.0001	0.9999
F81	38	-715.9886	1644.5763	0.0000	1.0000
SYM	40	-711.3684	1646.5253	0.0000	1.0000
F81IG	40	-711.4450	1646.6784	0.0000	1.0000
JC69G	36	-722.8455	1647.1007	0.0000	1.0000
JC69I	36	-722.9682	1647.3459	0.0000	1.0000
JC69	35	-726.2174	1648.2497	0.0000	1.0000
SYMIG	42	-706.7313	1648.4405	0.0000	1.0000
JC69IG	37	-722.8105	1652.6254	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_3148.phylip = 1 - 269;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_3148.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_3148.phylip = 1 - 269;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_3148.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 BIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_3148.phylip = 1 - 269;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_3148.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

