bioinfo-tools.md

What bioinformatics tools are out there?

There are more bioinformatics tools, Horatio, than are dreamt of in your philosophy ~ William Shakespeare, if he were a bioinformatician

The best way to find bioinformatics tools is to comb through papers and look for the link to the software implementation. Many bioinformatics journals require the source code to be publicly available on repositories such as GitHub and Bitbucket. If you are just starting out on an area, it may be helpful to first be acquainted with the lay of the land by reading survey papers.

There are dedicated repositories for bioinformatics tools such as bio.tools. Nucleic Acids Research also publishes an annual issue on bioinformatics web servers (read the 2024 issue here).

With the plethora of available tools, shortlisting tools can be a challenge. Here is a guide to tool selection:

• https://davetang.org/muse/2023/07/12/deciding-which-bioinformatics-tool-to-use/

Below are some of the tools that have been used by our lab for common bioinformatics tasks. This list is only intended to be a starting point. Our understanding of life evolves, novel approaches are introduced, and new tools are developed every day.

Sequence Alignment

• BLAST
  • Paper: https://www.sciencedirect.com/science/article/abs/pii/S0022283605803602
  • Website: https://blast.ncbi.nlm.nih.gov/Blast.cgi
• LAST
  • Paper: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-papers.rst
  • Website: https://gitlab.com/mcfrith/last

Sequence Clustering

• CD-HIT
  • Paper: https://academic.oup.com/bioinformatics/article/22/13/1658/194225
  • Website: https://sites.google.com/view/cd-hit
• MMseqs2
  • Paper: https://www.nature.com/articles/nbt.3988
  • Website: https://github.com/soedinglab/MMseqs2

Protein Structure Prediction

• AlphaFold

  • Paper: https://www.nature.com/articles/s41586-021-03819-2
  • Website: https://deepmind.google/technologies/alphafold/

• ColabFold

  • Paper: https://www.nature.com/articles/s41592-022-01488-1
  • Website: https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb
  • For local installation: https://github.com/YoshitakaMo/localcolabfold

Protein Structure Alignment

• US-align
  • Paper: https://www.nature.com/articles/s41592-022-01585-1
  • Website: https://zhanggroup.org/US-align/

Protein Structure Searching and Clustering

• Foldseek
  • Paper: https://www.nature.com/articles/s41587-023-01773-0
  • Website: https://github.com/steineggerlab/foldseek

Sequence Collection

• Phages
  • INPHARED
    • Paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9041510/
    • Website: https://github.com/RyanCook94/inphared

Gene Prediction

• Prokaryotes
  • Prodigal
    • Paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-119
    • Website: https://github.com/hyattpd/Prodigal

Genome Annotation

• Viruses
  • PHROG
    • Paper: https://academic.oup.com/nargab/article/3/3/lqab067/6342220
    • Website: https://phrogs.lmge.uca.fr/