software.qmd

---
title: "Bioinformatics Software tools"
image: ./assets/images/software.jpg
description: |
 Useful bioinformatics software tools
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about:
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    - icon: twitter
      text: Twitter
      href: https://twitter.com/scompbiol
    - icon: github
      text: Github
      href: https://github.com/sipbs-compbiol
    - icon: envelope
      text: Email
      href: mailto:leighton.pritchard@strath.ac.uk
html:
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---

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.

## Programming

- [Visual Studio Code](https://code.visualstudio.com/) - _An excellent editor for writing your own code, in any language, with support for a wide range of helpful extensions - LP_
- [Anaconda](https://www.anaconda.com/) - _A data science platform supporting Python, R, and other languages, that is cross-platform and simplifies installing some packages - LP_
- [Project Jupyter](https://jupyter.org/) - _A standard framework for coding in a notebook format - LP_
- [Snakemake](https://snakemake.github.io/) - _Reproducible bioinformatics analysis framework - LP_
- [NextFlow](https://www.nextflow.io/) - _Reproducible, scalable computational analysis framework - LP_

### Python

- [Biopython](https://biopython.org/) - _The standard bioinformatics packages for Python - LP_

### R

- [CRAN](https://cran.r-project.org/) - _The Comprehensive R Archive Network - it's where to go for `R` packages - LP_
- [Posit/RStudio](https://posit.co/) - _The makers of `RStudio` - the user-friendly way to use `R` - LP_
- [Bioconductor](https://www.bioconductor.org/) - _`R`'s compendium of computational biology software - LP_

## Online tool collections

- [Galaxy (Europe)](https://usegalaxy.eu/) - _The European Galaxy service for scientific workflows - LP_
- [EBI Tools](https://www.ebi.ac.uk/services) - _European Bioinformatics Institute online tool collection - LP_

## Sequence Analysis

- [NCBI BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi) - _NCBI's BLAST service - LP_
- [JalView](https://www.jalview.org/) - _Widely-used sequence analysis platform - LP_
- [PolyView](https://polyview.cchmc.org/) - _Coevolution and protein structure annotation server - LP_
- [CoevLab](https://research.cchmc.org/CoevLab/) - _Protein covariation analysis server - LP_
- [ibis2analyzer](http://ibis2analyzer.lcqb.upmc.fr/#/) - _Phylogenetically-informed covariation analysis server - LP_
- [ConSurf](http://consurf.tau.ac.il/overview.html) - _Evolutionary conservation estimation tool - LP_

### Sequence Alignment

- [MAFFT](https://mafft.cbrc.jp/alignment/software/) - _Fast multiple sequence alignment package - LP_
- [T-COFFEE](https://tcoffee.org/Projects/tcoffee/index.html) - _Very capable and diverse multiple sequence alignment package - LP_
  - [T-COFFEE online server](https://tcoffee.crg.eu/)
- [Clustal Omega](http://www.clustal.org/omega/) - _Fast multiple sequence alignment package - LP_

## Protein Structure

- [AlphaFold Colab](https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb?pli=1) - _Public interface to AlphaFold structural prediction - LP_
- [SWISSMODEL](https://swissmodel.expasy.org/) - _Structural homology modelling server - LP_
- [DeepView/Swiss PDB Viewer](https://spdbv.unil.ch/) - _Protein structure visualisation that integrates with SWISSMODEL - LP_
- [PyMol](https://pymol.org/2/) - _Standard package for visualising and analysing protein structure - LP_
- [UCSF Chimera](https://www.cgl.ucsf.edu/chimera/) - _Very capable structure visualisation and modelling package - LP_
- [RCSB-PBS's list of molecular graphics software](https://www.rcsb.org/docs/additional-resources/molecular-graphics-software) - _Comprehensive list of structure visualisation options - LP_

## Phylogenetics

- [IQ-TREE](http://www.iqtree.org/) - _Maximum-likelihood phylogenetic reconstruction - LP_
- [RAxML](https://github.com/amkozlov/raxml-ng) - _Maximum-likelihood phylogenetic reconstruction - LP_
- [SplitsTree](https://uni-tuebingen.de/en/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/splitstree/) - _Recombination-aware phylogenetic reconstruction - LP_
- [FigTree](http://tree.bio.ed.ac.uk/software/Figtree/) - _Lightweight phylogenetic tree visualisation - LP_
- [Dendroscope](https://uni-tuebingen.de/en/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/dendroscope/) _Very capable phylogenetic tree viewer - LP_