Bioinformatics Language Benchmark


This benchmark compares the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Needleman-Wunsch algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python.
A survey ( on which languages would be the most useful to learn ranked the following languages in decreasing order: Python, Perl, Java, C/C++ and the framework .NET which includes C#.


  • 6 programming languages: C, C++, C#, Java, Perl, Python
  • 3 programs: Needleman-Wunsch global alignment algorithm, Neighbor-Joining tree algorithm and BLAST parsing program.
  • 2 Operating Systems: Linux (Fedora) and Windows (XP)