BLAST computes a pairwise alignment between a query and the database sequences searched. It does not explicitly compute an alignment between the different database sequences (i.e., does not perform a multiple alignment). For purposes of this sequence tree presentation an implicit alignment between the database sequences is constructed, based upon the alignment of those (database) sequences to the query. It may often occur that two database sequences align to different parts of the query, so that they barely overlap each other or do not overlap at all. In that case it is not possible to calculate a distance between these two sequences and only the higher scoring sequence is included in the tree.
Download:
Downloads the guide tree into a text file in Newick or Nexus format (recognized by popular phylogenetic analysis software).
Node labels can be changed with the Sequence Label option (below, to the right).
Internal nodes whose all children have the same blast name and subtrees collapsed by a user are labeled with Blast Name.
Note: Newick and Nexus formats do not support collapsed subtrees, therefore fully expanded tree is always downloaded.