I am writing a biological evolution simulator. Currently, all my code is written in Python. For the most part, this is great and everything works quite well. However, there are two steps in this process that take a lot of time and which I would like to rewrite in Scala.
The first area of concern is the evolution of sequence. Imagine that you are given a phylogenetic tree that binds a large set of proteins. The length of each branch represents the evolutionary distance between the parent and the child. The root of the tree is seeded with one sequence, and then the evolutionary model (for example, http://en.wikipedia.org/wiki/Models_of_DNA_evolution ) is used to evolve the sequence along the tree structure; taking into account the lengths of the branches. PyCogent takes a long time to complete this step, and I believe that a reasonable implementation of Java / Scala will be significantly faster. Do you know of any libraries that implement this type of functionality. I want to write an application in Scala, so due to compatibility any Java library will be sufficient.
The second problem area is the comparison of generated sequences. The problem is that, given the set of sequences for proteins in a number of different extant species, try using the sequence to restore the phylogenetic tree that binds this species. This problem inherently requires computational requirements, because basically it is necessary to conduct pairwise comparisons between all sequences in existing species. However, again, I feel that the Java / Scala implementation will run much faster than Python, if nothing more than, unfortunately, the slow cycle speed in Python. This part, which I could write from scratch more easily than the part of the evolution of the sequence, but I would be ready to use the library for it, if there is a good one.
Thanks Rob