Purpose: This tool takes a nucleotide sequence alignment, converts it to NEXUS format, and uses PAUP to generate a tree, which is displayed using the PHYLIP programs Drawgram or Drawtree.
Details: Gaps can be treated as missing or stripped. The user can choose from various distance models and set the number of the outgroup sequence. A version of the input alignment in which the sequences have been reordered to match the order in the tree may be downloaded. Trees are calculated using the neighbor-joining method. You can use our FindModel tool to decide which of the offered models best fit your data.
Disclaimer: This interface only offers very basic, 'quick-and-dirty' phylogenetic analysis. More in-depth analysis is usually needed. For more information see the Tree Tutorial.
The HIV TreeMaker page has moved to:
HIV Neighbor TreeMaker.