This page provides links to software tools and packages - some with web interfaces, some you would need to download and install - that may be useful for your project.
1 Programming
- Visual Studio Code - An excellent editor for writing your own code, in any language, with support for a wide range of helpful extensions - LP
- Anaconda - A data science platform supporting Python, R, and other languages, that is cross-platform and simplifies installing some packages - LP
- Project Jupyter - A standard framework for coding in a notebook format - LP
- Snakemake - Reproducible bioinformatics analysis framework - LP
- NextFlow - Reproducible, scalable computational analysis framework - LP
1.1 Python
- Biopython - The standard bioinformatics packages for Python - LP
1.2 R
- CRAN - The Comprehensive R Archive Network - it’s where to go for
Rpackages - LP - Posit/RStudio - The makers of
RStudio- the user-friendly way to useR- LP - Bioconductor -
R’s compendium of computational biology software - LP
2 Online tool collections
- Galaxy (Europe) - The European Galaxy service for scientific workflows - LP
- EBI Tools - European Bioinformatics Institute online tool collection - LP
3 Sequence Analysis
- NCBI BLAST - NCBI’s BLAST service - LP
- JalView - Widely-used sequence analysis platform - LP
- PolyView - Coevolution and protein structure annotation server - LP
- CoevLab - Protein covariation analysis server - LP
- ibis2analyzer - Phylogenetically-informed covariation analysis server - LP
- ConSurf - Evolutionary conservation estimation tool - LP
3.1 Sequence Alignment
- MAFFT - Fast multiple sequence alignment package - LP
- T-COFFEE - Very capable and diverse multiple sequence alignment package - LP
- Clustal Omega - Fast multiple sequence alignment package - LP
4 Protein Structure
- AlphaFold Colab - Public interface to AlphaFold structural prediction - LP
- SWISSMODEL - Structural homology modelling server - LP
- DeepView/Swiss PDB Viewer - Protein structure visualisation that integrates with SWISSMODEL - LP
- PyMol - Standard package for visualising and analysing protein structure - LP
- UCSF Chimera - Very capable structure visualisation and modelling package - LP
- RCSB-PBS’s list of molecular graphics software - Comprehensive list of structure visualisation options - LP
5 Phylogenetics
- IQ-TREE - Maximum-likelihood phylogenetic reconstruction - LP
- RAxML - Maximum-likelihood phylogenetic reconstruction - LP
- SplitsTree - Recombination-aware phylogenetic reconstruction - LP
- FigTree - Lightweight phylogenetic tree visualisation - LP
- Dendroscope Very capable phylogenetic tree viewer - LP