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ClustalW FAQ (Frequently Asked Questions)
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How
can I save the guide tree image or the jalview alignment?
The only way this can be done is by making a screen
shot. This is because applets are not printed out with the html pages. You will need to: - Use the "Print Screen" button in the top right
corner of your keyboard.
- * Open an imaging application like paintshoppro or
photoshop.
- * Go "file>new" from the menu or
"control+N" from the keyboard to create a new image. Go
"edit>paste from the menu or "control+V" from the keyboard to
paste your screen capture.
- >*
The use the crop function to trim the image (e.g. "image>crop"). *
Then save or print the image.
What
is the difference between a cladogram and a phylogram?
A phylogram is a branching diagram (tree) that is
assumed to be an estimate of a phylogeny. The branch lengths are proportional
to the amount of inferred evolutionary change. A cladogram is a branching
diagram (tree) assumed to be an estimate of a phylogeny where the branches are
of equal length. Therefore, cladograms show common ancestry, but do not
indicate the amount of evolutionary "time" separating taxa. It is
possible to see the tree distances by clicking on the diagram to get a menu of
options. The options available allow you to do things like changing the colours
of lines and fonts and showing the
distances.
Which method is used to draw the guide tree?
The method names PHYLIP is the equivalent of new hamshire format tree representation. All clustalw phylogenetic calculations are based around the neighbor-joining method of Saitou and Nei.
Is there an alternative tree drawing program that can be used for large numbers of sequences?
If the number of sequences is very large, the default tree drawing program can generate an image that is too large to capture with print screen. In these situations a number of other programs may help to scale the
image down:
http://pearl.cs.pusan.ac.kr/phylodraw/
http://pfaat.sourceforge.net/
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
You will need to install the application on your PC. Then save your ClustalW tree file (.ph) and use it with the application.
Is it possible to perform bootstrap analysis or to get the Bootstrap values along with the nodes of each branch of the phylogram?
No - bootstrap analysis is too cpu intensive so we do not allow it via the website
If you do wish to do this you will need to download the software (available from the clustal page) and run this locally.
Can we have distance scale (as bar) based on the substitution rates along with the phylogram?
We do not produce a bar but distances can be displayed when you right click on
the java applet
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