Phylogenetic Tree

• The UPGMA method which assumes that evolution has occurred at a constant rate in the different lineages. This means that a root of tree is also estimated.
• The neighbor-joining method which builds a tree where the evolutionary rates are free to differ in different lineages.

To evaluate the reliability of the inferred tree, the option of doing a bootstrap analysis is allowed. A bootstrap value is attached to each branch, and this value is a measure of confidence in this branch. The maximum value is 100.

The following layout options are available when viewing a phylogenetic tree:

• Tree layout:
  • Choice of standard or topology layout
  • Size of tree (from tiny to huge)
• Annotation layout:
  • Node annotation (name or species)
  • Branch annotation (none, branch, length, or bootstrap)
  • Justification (left, center or right)
• Rearrange the vertical order of the sequences in the tree
• Adjust the length of the branches
• Change the root of the tree
• Collapse/uncollapse branches

Read more

• Bioinformatics Explained: Phylogenetics
  Memo describing some of the theories behind phylogenetics
• Overview of our software products
• Short description of CLC Sequence Viewer
• Receive more information as our programs evolve