LBA was first recognized as problematic when analyzing discrete morpological character sets under parsimony criteria, however Maximum Likelihood analyses of DNA or protein sequences are also susceptible. A simple hypothetical example can be found in Felsenstein 1978 where it is demonstrated that for certain unknown "true" trees, some methods can show bias for grouping long branches, ultimately resulting in the inference of a false sister relationship. Often this is because convergent evolution of one or more characters included in the analysis has occurred in multiple taxa. Although they were derived independently, these shared traits can be misinterpreted in the analysis as being shared due to common ancestry.
In phylogenetic and clustering analyses, LBA is a result of the way clustering algorithms work: terminals or taxa with many autapomorphies (character states unique to a single branch) may by chance exhibit the same states as those on another branch (homoplasy). A phylogenetic analysis will group these taxa together as a clade unless other synapomorphies outweigh the homoplastic features to group together true sister taxa.
These problems may be minimized by using methods that correct for multiple substitutions at the same site, by adding taxa related to those with the long branches that add additional true synapomorphies to the data, or by using alternative slower evolving traits (e.g. more conservative gene regions).
The result of LBA in evolutionary analyses is that rapidly evolving lineages may be inferred to be closely related, regardless of their true relationships. For example, in DNA sequence-based analyses, the problem arises when sequences from two (or more) lineages evolve rapidly. There are only four possible nucleotides and when DNA substitution rates are high, the probability that two lineages will evolve the same nucleotide at the same site increases. When this happens, parsimony may erroneously interpret this homoplasy as a synapomorphy (i.e., evolving once in the common ancestor of the two lineages).
The opposite effect may also be observed, in that if two (or more) branches exhibit particularly slow evolution among a wider, fast evolving group, those branches may be misinterpreted as closely related. As such, "long branch attraction" can in some ways be better expressed as "branch length attraction". However, it is typically long branches that exhibit attraction.
The recognition of long-branch attraction implies that there is some other evidence that suggests that the phylogeny is incorrect. For example morphological data may suggest that taxa marked as closely related are not truly sister taxa. Hennig's Auxiliary Principle suggests that synapomorphies should be viewed as de facto evidence of grouping unless there is specific contrary evidence (Hennig, 1966; Schuh and Brower, 2009).
A simple and effective method for determining whether or not long branch attraction is affecting tree topology is the SAW method, named for Siddal and Whiting. If long branch attraction is suspected in a pair of taxa (A and B), simply remove taxon A ("saw" off the branch) and re-run the analysis. Then remove A and replace B, running the analysis again. If either of the taxa appear at different branch points in the absence of the other, there is evidence of long branch attraction. Since long branches can't possibly attract one another when only one is in the analysis, consistent taxon placement between treatments would indicate long branch attraction is not a problem.