Bonsai Task-Oriented Help

Construct a de novo Multiple Alignment from a set of sequences: Use the Bonsai main window to load the sequences from a file. Fasta is the Bonsai external-exchange sequence format. If you want, select "Settings : Pair Alignment Settings" to change the default settings that will be used to perform the pairwise alignments that underlie the guide tree. Use "Settings : Multiple Alignment Settings" to change the default settings used in the multiple alignment phase of the alignment. It will rarely be desirable to change the default score matrices, but you may often want to display a different set of results using these Settings panels. After the first-pass multiple alignment is complete, it is usually desirable to use "Align : Progressively Refine" from the main alignment window. If the sequences are highly divergent, you may continue to get improved alignments by more than one progressive refinement. Keep an eye on whether the alignment score improves.

Construct a new Phylogenetic Tree from a set of sequences: Follow instructions above for constructing a de novo multiple alignment, then in the Score-shaded Multiple Alignment window, use "Calculate : N-J Tree from multiple alignment" to compute a phylogenetic tree. This tree is computed by deriving pairwise alignments from the multiple alignment shown, computing each of their scores, making distance corrections, and using the Neighbor-Joining method to cluster the pairs into a tree. An alternative, desirable if the Multiple alignment seems deranged in some way (not infrequent if the sequences are extremely divergent - check by eye) is to use the guide tree as your phylogenetic tree.

Align sequences to an existing profile: In the main window of Bonsai, load the sequences you want to align and then use "Align : Align Sequences to Profile". You will be prompted to load the profile from a file. Currently, the profile must be in Bonsai format (created with Bonsai). I will extend this to handle some standard multiple alignment formats and I plan to add a set of prealigned profiles for common sequence classes for use (e.g. kinases, serine proteases, nuclear hormone receptors). You can also do this type of alignment from an already-loaded profile from its Score-shaded Multiple Alignment window.

Align a profile to another profile: Use the Bonsai main window to open one of the profiles using "File : Load Profile".Then, in the Score-shaded Multiple Alignment window, use "Align : Align a Profile to this Profile" to load and align to a second profile. Each parent profile and their alignment to each other will each be shown in Score-shaded Multiple Alignment windows.

[NOT FUNCTIONAL Extend an existing Phylogenetic Tree: This procedure requires that the existing tree is fully sequence- and alignment-backed (if it is not, simply combine all the sequences in one list and compute the complete tree). Load the sequences you want to add to the existing tree, then use "Align : Extend Pairwise Tree". You will be prompted to load an existing tree, which must be in Bonsai format (.bnst file). NOTE - if the pairwise alignment parameters are not the same as for the previous tree you will obtain distorted results!]

Edit Sequences: Bonsai is not set up for sophisticated sequence editing, but a few basic operations can be performed. When a list of sequences is loaded, you can easily append more sequences from a file or delete existing sequences using the File and Edit menus. You can view and edit the name and residue sequence of any sequence by selecting it and using "Show : Selected Sequence Properties". You can change the sequence name or sequence itself by clicking and editing the appropriate fields. You can also add comments to the box below the sequence. Currently these will be saved only if you save the file in Bonsai format. BE SURE to click "Record Changes" before closing if you want to save any additions or changes! There isn't yet any safety check.


Links to other tasks:

- use the sequence evolution simulator

- arrange an existing phylogenetic tree to produce a figure

- use the dot matrix to select sequence blocks

- use the phylogenetic tree distance corrector

- move gaps in a multiple alignment by hand

- edit the scores and weights in a PSSM


James H. Thomas, Department of Genome Sciences, University of Washington
11/14/2002