Here below are the list of softwares I found to be very handy for applied bioinformatics. Most of the tools I listed here are open-source program.

  • PRANK - Codon sequence alignment
  • MAFFT - Multiple sequence alignment, similar performance to MUSCLE
  • egglib - powerful tools for population genetics and genomics data analysis
  • Roary - tool for pan-core genome study (bacteria primarily)
  • Prodigal - is bacterial genome annotation tool, which works seamlessly with Roary.
  • ete - a nice phylogenomics tool kit with API to python
  • Bioconda bioinfo software package manager and environmental manager
  • d-maps high quality map images, multiple format supported
  • R-Bioconductor
  • To be continued