System Details: WinXP SP2, ATI MOBILITY RADEON X300, 1GB RAM

[James comments, bugs in TreeJuxtaposerBugs are numbered]

Activity Log:

1. Added gl4Java .dlls and .jars to JRE 1.4.2_08, used WinZip to directly extract, however this created another directory gl4java. I had to use Windows Explorer to move dlls and jars up a directory.
2. Downloaded TreeJuxtaposer executable jar v1.3. JFrame Title bar showed v1.2 [versioning, known bug]
3. Looked at input: requires Newick/Nexus format.
4. Loaded a DND file from a ClustalW analysis to the TJ
5. TJ didn't recognize the *.dnd file as a Newick? [add .dnd to newwick types. Are there other extensions?] type so had to use "All files" to load. This loaded successfully.
6. It is GL thing likely, but the settings panel flipped back when I opened it to the lower window (didn't stay on top). Also couldn't drag it over the TJ window without it disappearing. This was happened with other frames/ popups. [3. this doesn't happen in linux with jogl, more testing needed. This certainly happened with gl4java on windows xp]
7. Settings changed main TJ panel in realtime. That was convenient for figuring out what the settings did.
8. I tried dragging one of the tree nodes on the TJ panel. It collapsed some labels. I then moved it back so I could see everything again. Wasn’t quite sure what I could/couldn’t do on the main tree visualization window
9. Loaded same alignment again. Saw split panel of two exactly the same trees. I am now going to attempt to try to figure out the differences between them.
10. Noticed that selecting a node on one tree selects nodes on both trees.
11. No idea what "Groups" does. I can guess that it groups something. Not sure if I want to do this. So I didn't.
12. Used find. Found a tag. Couldn't deselect it once highlighted. [2. no way to hide found groups without clearing] I tried right clicking on TJ panel. No dice. I tried clicking on tag, right-clicking on tag. No dice. Wait it isn't tag that is highlighted it is the small branch to the tag/label that stays pink. [1. no way to clear found items]
13. Decided that two trees of the same alignment are not showing me much in terms of differences. I then tried two different alignment trees. Saw red difference bars. Okay, so the differences are calculated on the fly. That makes sense.
14. Could be a hardware issue but I saw panels like this: [4. more than likely a redraw problem]
15. Going to try for a real group now as I mentioned in previous email. The first image is the raw alignment. The second is optimized so that the strandedness of the sequences maximizes the alignment score.

It seems like there are lots of differences between these alignments. Where these alignments are centred about in the human genome from left-to-right:

chr1 168353534 168353534

chr1 168353632 168353632

chr1 168353793 168353793

chr1 168355490 168355490

chr1 168358095 168358095

chr1 168358598 168358598