emboss-kaptain has a dependency on embassy-phylip, which is blocked by embassy-4.0.0. The dependency should be changed to embassy-phylipnew in the ebuild.
This is is now fixed in emboss-kaptain-0.97-r2. Thanks for reporting, and sorry for the delay (quite a number of fixes were required). However, the ebuild is package masked as there are a number of issues that remain with PHYLIP, emma and probably a few other packages/programs. With EMBOSS-Kaptain unmaintained upstream and the EMBOSS team streamlining the command-line interfaces to many programs in the latest versions, I doubt we will want to keep this in Portage much longer, unless someone wants to invest the necessary time to review the grammar files and ensure they conform to the EMBOSS ACD files.