
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:25 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_5501.phylip" (19 taxa, 609 characters)

Minimum AIC  model: GTRIG
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	-1676.7737	3448.5687	0.2685	0.2685
GTRIG	45	-1675.6604	3448.6743	0.2547	0.5232
HKYIG	41	-1680.5643	3449.2027	0.1956	0.7188
HKYG	40	-1681.7766	3449.3278	0.1837	0.9025
GTRI	44	-1678.4051	3451.8314	0.0525	0.9550
HKYI	40	-1683.1840	3452.1426	0.0450	1.0000
F81IG	40	-1705.0657	3495.9060	0.0000	1.0000
F81G	39	-1706.3813	3496.2459	0.0000	1.0000
F81I	39	-1707.6892	3498.8617	0.0000	1.0000
GTR	43	-1706.1759	3505.0492	0.0000	1.0000
K2PIG	38	-1712.0158	3505.2315	0.0000	1.0000
K2PG	37	-1713.4482	3505.8212	0.0000	1.0000
HKY	39	-1711.5485	3506.5804	0.0000	1.0000
K2PI	37	-1714.7483	3508.4214	0.0000	1.0000
SYMIG	42	-1711.3992	3513.1800	0.0000	1.0000
SYMG	41	-1712.6078	3513.2896	0.0000	1.0000
SYMI	41	-1713.6648	3515.4036	0.0000	1.0000
JC69G	36	-1734.4458	3545.5490	0.0000	1.0000
JC69IG	37	-1734.0127	3546.9500	0.0000	1.0000
JC69I	36	-1736.6248	3549.9069	0.0000	1.0000
F81	38	-1735.8050	3552.8099	0.0000	1.0000
K2P	36	-1744.5233	3565.7039	0.0000	1.0000
SYM	40	-1742.5788	3570.9323	0.0000	1.0000
JC69	35	-1765.1141	3604.6262	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1675.6604	3441.3209	0.3472	0.3472
GTRG	44	-1676.7737	3441.5474	0.3100	0.6572
HKYIG	41	-1680.5643	3443.1286	0.1406	0.7978
HKYG	40	-1681.7766	3443.5532	0.1137	0.9115
GTRI	44	-1678.4051	3444.8101	0.0607	0.9722
HKYI	40	-1683.1840	3446.3679	0.0278	1.0000
F81IG	40	-1705.0657	3490.1314	0.0000	1.0000
F81G	39	-1706.3813	3490.7626	0.0000	1.0000
F81I	39	-1707.6892	3493.3784	0.0000	1.0000
GTR	43	-1706.1759	3498.3518	0.0000	1.0000
K2PIG	38	-1712.0158	3500.0315	0.0000	1.0000
K2PG	37	-1713.4482	3500.8965	0.0000	1.0000
HKY	39	-1711.5485	3501.0971	0.0000	1.0000
K2PI	37	-1714.7483	3503.4967	0.0000	1.0000
SYMIG	42	-1711.3992	3506.7984	0.0000	1.0000
SYMG	41	-1712.6078	3507.2155	0.0000	1.0000
SYMI	41	-1713.6648	3509.3295	0.0000	1.0000
JC69G	36	-1734.4458	3540.8917	0.0000	1.0000
JC69IG	37	-1734.0127	3542.0253	0.0000	1.0000
JC69I	36	-1736.6248	3545.2496	0.0000	1.0000
F81	38	-1735.8050	3547.6099	0.0000	1.0000
K2P	36	-1744.5233	3561.0465	0.0000	1.0000
SYM	40	-1742.5788	3565.1576	0.0000	1.0000
JC69	35	-1765.1141	3600.2283	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1681.7766	3620.0259	0.7238	0.7238
HKYI	40	-1683.1840	3622.8407	0.1772	0.9010
HKYIG	41	-1680.5643	3624.0131	0.0986	0.9996
GTRG	44	-1676.7737	3635.6674	0.0003	0.9999
GTRI	44	-1678.4051	3638.9301	0.0001	1.0000
GTRIG	45	-1675.6604	3639.8527	0.0000	1.0000
F81G	39	-1706.3813	3662.8235	0.0000	1.0000
K2PG	37	-1713.4482	3664.1337	0.0000	1.0000
F81I	39	-1707.6892	3665.4393	0.0000	1.0000
F81IG	40	-1705.0657	3666.6041	0.0000	1.0000
K2PI	37	-1714.7483	3666.7340	0.0000	1.0000
K2PIG	38	-1712.0158	3667.6806	0.0000	1.0000
HKY	39	-1711.5485	3673.1580	0.0000	1.0000
GTR	43	-1706.1759	3688.0600	0.0000	1.0000
SYMG	41	-1712.6078	3688.1001	0.0000	1.0000
SYMI	41	-1713.6648	3690.2141	0.0000	1.0000
SYMIG	42	-1711.3992	3692.0947	0.0000	1.0000
JC69G	36	-1734.4458	3699.7171	0.0000	1.0000
JC69I	36	-1736.6248	3704.0750	0.0000	1.0000
JC69IG	37	-1734.0127	3705.2626	0.0000	1.0000
F81	38	-1735.8050	3715.2590	0.0000	1.0000
K2P	36	-1744.5233	3719.8720	0.0000	1.0000
SYM	40	-1742.5788	3741.6304	0.0000	1.0000
JC69	35	-1765.1141	3754.6419	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_5501.phylip = 1 - 609;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_5501.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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_5501.phylip = 1 - 609;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_5501.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_5501.phylip = 1 - 609;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_5501.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

