Version 6.2.0 of EMBOSS now includes the capability to read additional file formats as well as updated versions of current formats. There are a number of new capabilities, and some changes required in scripts. Details of these changes can be found at http://emboss.sourceforge.net/developers/changelog.html#0.

Macaulay2 now includes certification of new packages that have been approved for publication in peer-reviewed journals, as well as a large number of new programs and packages. Some capabilities have been improved or changed. Users should review http://www.math.uiuc.edu/Macaulay2/doc/Macaulay2-1.3.1/share/doc/Macaulay2/Macaulay2Doc/html/_changes_cm_sp1.3.html for details on these improvements.

R has been upgraded to 2.10.1. There are a number of new features as well as a long list of bugfixes. For specifics refer to https://svn.r-project.org/R/trunk/NEWS (scroll down to 2.10 and 2.10.1). Many R-related packages and emacs modes have also been upgraded.

Fedora 13 includes version 1.6.1 of ugene. The upgrade is strongly recommended as there are some fixes to serious bugs. If you prefer to compile the package rather than installing from the RPM, you should review http://ugene.unipro.ru/news.html#160210 for specific actions that you need to take to make the upgrade successful. This is not necessary for a normal install using yum or PackageKit.