What's with 'Z's that appear in the alignment?
They denote exon boundaries.
 
Downloading alignments and viewing them locally
The links above the alignment visualization window can be used to download the alignments, either peptide or nucleotide, and use them locally.
 
  ●   Left mouse click to open the alignment as a text file in the browser. Right mouse click to 'Save as.' (A special note for Safari users: when you are right clicking/saving, make sure to choose "Page Source" from the format menu, rather than "Web Archive.")
  ●   To view and manipulate an alignment you can use e.g. Seaview, a lightweight and user-friendly application. For other alignment viewers, Wikipedia provides a good starting point.
 
However, before you plunge into installing your own sequence editor ...
Jalview, used by ExoLocator to display the alignments, is a capable and versatile sequence editor you can use to manipulate the alignment right there in the browser. Note the drop-down menus you can choose from. Check out Jalview's documentation page.
 
"But JalView is not working in my browser!"
Yes Jalview, and Java applets in general can be a headache. First try here, for a nice illustration of how JalView should be working, from the authors themselves. If it works fine while the JalView applet in ExoLocator does not (in the same browser, and on the same computer), send us a note.
 
If the JalView demo does not work, most likely Java on your computer needs to be updated. See the hints at the bottom of this page.
 
Using alignments as input for conservation and specialization scoring
   The alignments produced by Exolocator can be used to score residue conservation within a group of orthologous sequences, or specialization between two groups of paralogues. From Exolocator itself, it can be done by clicking on the conservation/specialization links, which forward the alignment to Cube server.
   The purpose of such exercise is, typically, to help in the rational design of single-site mutational experiments, to estimate the impact of SNPs, or guide computational docking. Specialization analysis, in particular, may help in the search of separation-of-function mutants.
   Follow this link to read more about why-and-how of protein sequence comparison.
 
" ... actually, I am not really sure what these ortho- and para-thingies are ..."
Check out the mini-presentation here.
 

 
Java updating hints. If the JalView demo does not work, most likely Java on your computer needs to be updated. Here are some hints.
  ●  The download page for Java can be found here..
  ●  Download the package for your operating system.
  ●  Unpack (the actual procedure depends on the platform - if everything else fails, follow the instructions) and restart the browser.
  ●  Verify Java installation here.
  ●  Again, check the demo. You may have to "accept the risk" of running the applets.
  ●  Return to ExoLocator.

If it still does not work, for MacOSX in particular, here is what can be gleaned on the Internet (from this source):
  ●   Under either OSX 10.8.3 or 10.7.5, Java 7-17 runs under Firefox 19.02.
  ●   Under either OSX 10.8.3 or 10.7.5, Java 7-17 does not run under Safari 6.0.3.
  ●   Under either OSX 10.8.3 or 10.7.5, Java 7-17 does not run under Chrome 25.x (Chrome is 32 bit, Java is 64 bit only).
If you are in posession of one of the unlucky combinations above, try Firefox.
and here are some notes from our own practice:

 Java JRE and plugin installation:

Ubuntu Linux
----------------
1. Run Terminal
2. sudo add-apt-repository ppa:webupd8team/java
3. sudo apt-get update
4. sudo apt-get install oracle-java7-installer
5. In configuration window click OK,
   then accept Oracle Binary Code license terms by clicking Yes
6. Download will start (accept action by entering Y(es)). Wait for Installer to finish.
7. Open web page. Security Warning will pop up.
   Check "I accept the risk and want to run this app." and click Run

Windows 
----------------
1. To install browser plugin open http://java.com/en/download/
2. Click on "Free Java Download" and then "Agree and Start Free Download"
3. In downloads folder double-click on:
   - chromeinstall-7u45.exe - for Google Chrome
   - jre-7u45-windows-x64 - for Internet Explorer 64-bit
   - jre-7u45-windows-i586 - for Internet Explorer 32-bit
   If UAC (User Account Control) window pops up click Yes to allow Installer to make changes to computer
4. In Java Setup window click Install (choose "Close Programs and Continue" if any browser windows are open)
5. This will also enable plugin for other browsers (like Mozilla Firefox or Internet Explorer*)
6. Restart of Web browser might be needed in order for plugin to become operational.
7. If security bar in browser asks for permission to run Java,
   you can click either "Run this time" or "Always run on this site"
8. Open web page. Security Warning will pop up.
   Check "I accept the risk and want to run this app." and click Run

9. If Jalview Applet loads for a very long time, try reloading current page


* On 64-bit Windows 64-bit version of Internet Explorer must be enabled:
1. In Control panel open Internet Options
2. On Security tab check "Enable Protected Mode"
3. On Advanced tab scroll the list and find and check "Enable Enhanced Protected Mode"
4. Close Internet Properties Window and restart computer