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--- | ||
title: "Bioinformatics Software tools" | ||
image: ./assets/images/software.jpg | ||
description: | | ||
Useful bioinformatics software tools | ||
number-sections: true | ||
about: | ||
template: marquee | ||
links: | ||
- 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:[email protected] | ||
html: | ||
anchor-sections: true | ||
--- | ||
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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. | ||
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## Programming | ||
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- [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_ | ||
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### Python | ||
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- [Biopython](https://biopython.org/) - _The standard bioinformatics packages for Python - LP_ | ||
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### R | ||
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- [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_ | ||
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## Online tool collections | ||
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- [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_ | ||
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## Sequence Analysis | ||
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- [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_ | ||
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### Sequence Alignment | ||
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- [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_ | ||
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## Protein Structure | ||
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- [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_ | ||
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## Phylogenetics | ||
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- [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_ |