This isn't a totally satisfactory solution, since kalign takes a pretty long time even though relatively simple alignments (this makes sense for an MSA library that was not designed for highly similar sequences). In addition, there seems to be a bug that right now I'm papering over in an ad hoc manner. However, kalign seems to be faster than some of the alternatives we looked into, and it can handle the memory requirements gracefully. Moreover, it was relatively easy to integrate it into this project.
Resolves https://github.com/vgteam/GetBlunted/issues/49.
This isn't a totally satisfactory solution, since kalign takes a pretty long time even though relatively simple alignments (this makes sense for an MSA library that was not designed for highly similar sequences). In addition, there seems to be a bug that right now I'm papering over in an ad hoc manner. However, kalign seems to be faster than some of the alternatives we looked into, and it can handle the memory requirements gracefully. Moreover, it was relatively easy to integrate it into this project.