The resulting algorithm thus provides sequences with realistic ASRV, substitution bias and correlation between sites. The tree conforms to a molecular clock, the long branches are due only to the absence of side branches. All of the tested algorithms are susceptible to long branch attraction. Use of maximum likelihood methods that incorporate both substitution bias and ASRV is superior over parsimony analysis. Test of algorithms for errors due to long branch attraction.
Bars indicate standard deviations calculated from independent simulations.
The better performance of some algorithms indeed appears to be due to the better extraction of phylogenetic information by these algorithms. Test of algorithms for long branch repulsion. For further explanations see text and table 1. The better performance of the used maximum likelihood approaches is also indicated in the results of Table 3. However, all of the algorithms performed surprisingly well, when the long branches were not due to unequal substitution rates but due to the absence of side branches.