Tree Method:
Algorithm used to produce a tree from given distances (or dissimilarities) between sequences. Available options:
1) Fast Minimum Evolution (Desper R and Gascuel O, Mol Biol Evol 21:587-98, 2004   PMID: 14694080)
2) Neighbor Joining (Saitou N and Nei M, Mol Biol Evol, 4:406-25, 1987   PMID: 3447015)
Note: Both algorithms produce un-rooted tree such as ones shown as radial or force in the tabs below. The rooted trees are created by placing a root in the middle of the longest edge.

Max Seq Difference:
The maximum allowed fraction of mismatched bases in the aligned region between any pair of sequences. If the fraction of mismatched bases for any pair of sequences is larger than this value, both sequences are excluded from tree generation. The link Show removed sequences (below to the right) shows those sequences. If the link is not shown, none of the sequences was excluded
Note: Distance between sequences used for tree generation predicts expected fraction of base substitutions per site given the fraction of mismatched bases in the aligned region. The accuracy of this prediction decreases as the fraction of mismatched bases increases. Hence for larger values of Max Seq Difference (> 0.5) sequence grouping is often accurate, but the lengths of paths between very dissimilar sequences can be inaccurate.

Sequence Label:
Text used in the tree to describe the sequences. Blast Names are informal high level taxonomic categories. The color of the terminal node indicates the Blast Name of a sequence.

Collapse Mode:
Reduction of the number of nodes in the tree by collapsing subtrees composed of nodes that belong to the same group. Options available:
1) Custom: collapsed subtrees are selected by a user (by selecting the option from tree node pop-up menu)
2) Blast Name: subtrees that contain sequences with common Blast Name are collapsed
3) Show All: the tree is fully expanded.
Note: The collapsed subtrees are shown as triangle nodes. The number of sequences in the collapsed subtree is shown in the label and reflected in node size.