Blast Tree View
This tree was produced using BLAST pairwise alignments. more...

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.

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.

Query ID

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.

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.

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.

Mouse over an internal node for a subtree or alignment. Click on tree label to select sequence to download
Label color map
Query highlight colorquery
Sequence of type highlight colorfrom type material
Show removed seqs
Sequences with more than 0.75 difference removed from treeview
gnl|BL_ORD_ID:5832 gnl|BL_ORD_ID:4955 gnl|BL_ORD_ID:4876
gnl|BL_ORD_ID:4852 gnl|BL_ORD_ID:4841 gnl|BL_ORD_ID:4834
gnl|BL_ORD_ID:4825 gnl|BL_ORD_ID:4818 gnl|BL_ORD_ID:4806
gnl|BL_ORD_ID:4793 gnl|BL_ORD_ID:4470 gnl|BL_ORD_ID:4337
gnl|BL_ORD_ID:4334 gnl|BL_ORD_ID:3920 gnl|BL_ORD_ID:511
gnl|BL_ORD_ID:298 gnl|BL_ORD_ID:35 gnl|BL_ORD_ID:5878
gnl|BL_ORD_ID:5812 gnl|BL_ORD_ID:5570 gnl|BL_ORD_ID:5562
gnl|BL_ORD_ID:4666 gnl|BL_ORD_ID:4523 gnl|BL_ORD_ID:3354
gnl|BL_ORD_ID:2844 gnl|BL_ORD_ID:2035 gnl|BL_ORD_ID:1909
gnl|BL_ORD_ID:1538 gnl|BL_ORD_ID:1538 gnl|BL_ORD_ID:1504
gnl|BL_ORD_ID:514 gnl|BL_ORD_ID:507 gnl|BL_ORD_ID:506
gnl|BL_ORD_ID:41 gnl|BL_ORD_ID:5784 gnl|BL_ORD_ID:4959
gnl|BL_ORD_ID:4642 gnl|BL_ORD_ID:3811 gnl|BL_ORD_ID:3811
gnl|BL_ORD_ID:3538 gnl|BL_ORD_ID:2541 gnl|BL_ORD_ID:2540
gnl|BL_ORD_ID:1914 gnl|BL_ORD_ID:277 gnl|BL_ORD_ID:5083
gnl|BL_ORD_ID:5083 gnl|BL_ORD_ID:3830 gnl|BL_ORD_ID:6067
gnl|BL_ORD_ID:5645 gnl|BL_ORD_ID:5513 gnl|BL_ORD_ID:5462
gnl|BL_ORD_ID:5036 gnl|BL_ORD_ID:4779 gnl|BL_ORD_ID:4690
gnl|BL_ORD_ID:4632 gnl|BL_ORD_ID:4601 gnl|BL_ORD_ID:4555
gnl|BL_ORD_ID:4537 gnl|BL_ORD_ID:4505 gnl|BL_ORD_ID:4495
gnl|BL_ORD_ID:4494 gnl|BL_ORD_ID:4492 gnl|BL_ORD_ID:4483
gnl|BL_ORD_ID:4462 gnl|BL_ORD_ID:4440 gnl|BL_ORD_ID:4346
gnl|BL_ORD_ID:4340 gnl|BL_ORD_ID:3979 gnl|BL_ORD_ID:3935
gnl|BL_ORD_ID:3735 gnl|BL_ORD_ID:3652 gnl|BL_ORD_ID:3613
gnl|BL_ORD_ID:2882 gnl|BL_ORD_ID:2879 gnl|BL_ORD_ID:2204
gnl|BL_ORD_ID:2037 gnl|BL_ORD_ID:354 gnl|BL_ORD_ID:326
gnl|BL_ORD_ID:37 gnl|BL_ORD_ID:5541 gnl|BL_ORD_ID:54
gnl|BL_ORD_ID:5433 gnl|BL_ORD_ID:4752 gnl|BL_ORD_ID:3653
gnl|BL_ORD_ID:3269 gnl|BL_ORD_ID:3170 gnl|BL_ORD_ID:3167
gnl|BL_ORD_ID:2869 gnl|BL_ORD_ID:1955 gnl|BL_ORD_ID:1915
gnl|BL_ORD_ID:143 gnl|BL_ORD_ID:5669 gnl|BL_ORD_ID:5241
gnl|BL_ORD_ID:5158 gnl|BL_ORD_ID:3963 gnl|BL_ORD_ID:3353
gnl|BL_ORD_ID:2901 gnl|BL_ORD_ID:2196 gnl|BL_ORD_ID:2021
gnl|BL_ORD_ID:2020 gnl|BL_ORD_ID:2015 gnl|BL_ORD_ID:2010
gnl|BL_ORD_ID:1998 gnl|BL_ORD_ID:1943 gnl|BL_ORD_ID:1941
gnl|BL_ORD_ID:831 gnl|BL_ORD_ID:623 gnl|BL_ORD_ID:147
gnl|BL_ORD_ID:55 gnl|BL_ORD_ID:3309 gnl|BL_ORD_ID:3305
gnl|BL_ORD_ID:308 gnl|BL_ORD_ID:3309 gnl|BL_ORD_ID:3305
Blast names color map
Selected sequences