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.
Required software for BM954 in AY2023-24
This year’s project students will be analysing the distribution and evolution of CAZymes across bacterial genomes. In order to do this, specialised packages are required, that were developed within this group. Please use the links below for documentation on how to install and use this software.
cazy_webscraper- a tool for collating and organising, in a local database, CAZymes and associated data (e.g. sequences, structures, etc.)cazomeevolve- a tool for analysing the evolution of CAZymes in microbial genomes
Relevant publications
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