Blast Tree View Widget

Tree view for RID: 97M9WCFS014, query ID: lcl|28963, database: refseq_genomic

Tree method [?]

Max Seq Difference [?]

in [?]

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.

Distance:
Evolutionary distance between two sequences modeled as expected fraction of amino acid substitutions per site given the fraction of mismatched amino acids in the aligned region. Distance models available:
1) Kimura (Kimura M, The neutral theory of molecular evolution, Cambridge University Press, Cambridge, UK, 1983): cannot be computed for fraction of mismatched bases larger than 0.75
2) Grishin (Grishin NV, J Mol Evol, 41:675-79, 1995 PMID: 18345592): approximates the same model as Kimura, but can be computed for fraction of mismatched amino acids larger than 0.75
3) Grishin General (Grishin NV, J Mol Evol, 41:675-79, 1995 PMID: 18345592): more general evolutionary model: substitution rates vary for both amino acids and sites.

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.

rectangle slanted radial force [?] Mouse over an internal node for a subtree or alignment

Methods for rendering tree. All the selections show the same guide tree computed with a method selected in the Tree method option (top left-hand corner).
1) Rectangle: rectangular shaped rooted tree, where root is places in the longest edge
2) Slanted: similar to rectangle, but with triangular tree shape
3) Radial: un-rooted tree
4) Force: similar to radial, where nodes are pushed away from one another for better presentation.

Sequence Label [?]

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.
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.

Blast names color map
	CFB group bacteria
	unknown