Tools for tree construction
The CLC Main Workbench includes three tools for generating phylogenetic trees:
- K-mer Based Tree Construction (
). Estimates evolutionary distances by comparing short sequence fragments (k-mers) directly, without requiring alignments or substitution models.
- Create Tree (
). Computes pairwise distances from a multiple sequence alignment, using substitution models. This results in more accurate distance estimates.
- Maximum Likelihood Phylogeny (
). Uses a sequence alignment along with evolutionary models and heuristic searches to estimate the tree that best explains the observed sequence data.
Note: A suitable substitution model to use can be identified by first running the Model Testing tool.
Subsections