Here's a rough list of the most recent changes to Cartwheel and FamilyRelationsII.

Note that you'll need to download the latest version of FRII to continue using Cartwheel; your older versions will no longer work.

• Cartwheel can now run blastz and LAGAN alignments, thus mimicking some of the functionality of PipMaker and VISTA, respectively. Pairwise VISTA comparisons can also be uploaded to the server but cannot be directly executed.

  You can see these new options on the normal pairwise comparison page where you would e.g. set up a seqcomp.

• You can zoom into the pairwise alignments for BLAST, blastz, and LAGAN/VISTA comparisons.

  Previously this zoom view was only supported for seqcomp comparisons.

• You can see reports on individual BLAST matches against a database, so that you can find out exactly what proteins or nucleotide sequences match to a particular location.

  This can be seen in "single view" mode, for new analyses; right-click (or ctrl-click, on Macs) on the sequence lines and select "single view". Then click on the feature(s) you're interested in. (Yes, the "single-view" option on the menus is new, too.)

• A fair amount of work was done to make the user interface more consistent, prettier, etc.

• A number of memory problems were fixed so FRII should crash less frequently!

Many of these changes are pretty significant and the functionality may be a bit fragile. Please let me know if you use the new features and run into problems. I'm always open to suggestions or comments, too!

--titus
titus@caltech.edu