A cladistic analysis typically requires the following steps. Though they may seem simple, each step actually requires a great deal of background knowledge and work.

1. Choose the taxa whose evolutionary relationships interest you. These taxa will be the tips of your tree and must themselves be clades. For example, you might choose 20 species of beetle that all fall within the same genus. Alternately, you might choose to reconstruct the relationships among the major clades of insects (beetles, flies, moths and butterflies, true bugs, dragonflies, etc.), where each taxon includes many species.

1. Determine the characters and examine each taxon to determine the character states. For example, you might select a suite of anatomical traits as your characters (e.g., number of segments in the antennae, presence of an upper vein on wing, etc.), and your character states would then be the different anatomical characteristics that your organisms have (e.g., has six antennal segments/has five antennal segments, has an upper vein/does not have an upper vein). Alternately, you might select the 362 bases in a particular gene as your characters, and your character states would then be A, T, G, or C for each of the 362 characters. Note that it is important to select characters that seem to be homologies, that is, characters that are similar because they were inherited from a common ancestor. Analogies, characters that evolved through convergent evolution in two separate lineages (like the dorsal fins of sharks and dolphins), are not useful for reconstructing phylogenies.
2. Determine the polarity of characters — in other words, figure out the order of evolution for each character. For example, did the beetle species under consideration all evolve from an ancestor with five antennal segments — and only later did six evolve, or was it the other way around? Did a lineage with six antennal segments evolve into a lineage with five? Figuring out the polarity of a character can take some work. In some situations, it is reasonable to assume that the character states in the outgroup are the ancestral states for the taxa of interest. In other situations, paleontologists may have fossil evidence that indicates the probable ancestral state of the character. Many different methods may be used to reason about character polarity. (Note that for some types of cladistic analysis, determination of character polarity is not absolutely necessary.)
3. Group taxa by synapomorphies, not by symplesiomorphies. Synapomorphies are derived or “changed” character states shared by two taxa. Symplesiomorphies are original character states shared by two taxa. So for example, imagine that we have determined that the common ancestor of our beetle clade had five antennal segments and passed that character state onto its immediate descendents: seven of the modern beetle species still have that character state. However, one lineage within the clade evolved six antennal segments and passed that character state onto its descendents — 14 of our beetle species. According to this rule, we would group the 14 beetle species with six segments together — but would not group the seven species with five segments together because this is the original character state.

1. Work out conflicts that arise by some clearly stated method, usually parsimony (more on this later).
2. Build your tree following these rules:
   • All taxa go on the endpoints of the tree, never at nodes.
   • All nodes must have a list of synapomorphies, which are common to all taxa above the node (unless the character is later modified).
   • All synapomorphies appear on the tree only once unless the character state was derived separately by evolutionary parallelism.
3. Voila! You have made a phylogeny. However, remember that this phylogeny is a hypothesis. It is supported by the available data, but new data or new interpretations of old data could change it! To be confident about your hypothesis, you must scrutinize your data by asking questions like these:
   • Could a supposed synapomorphy be the result of convergent evolution?
   • Do your characters make sense from an evolutionary perspective?
   • Should you consider other characters?
   • Should you consider additional taxa?