This page contains links to, and overviews of, software packages that are useful for students and lab members alike. I have attempted wherever possible to ensure that the software linked is free, and works on both Windows and Mac operating systems. Most will not work on a tablet, unfortunately.
Graphics
https://inkscape.org/ – InkScape, a vector editing software (for graphics)
https://www.gimp.org/ – GIMP, a raster editing software (for photos)
Stats and analysis (only Open Source)
https://posit.co/downloads/ – RStudio Desktop
https://imagej.net/software/fiji/ – Fiji, which is a ImageJ with extensions pre-installed
Micro-CT segmentation and analysis
https://www.theobjects.com/dragonfly/ – Dragonfly, software for segmentation. Free for academics.
https://www.slicer.org/ – 3D Slicer, software for segmentation. Can also do geometric morphometric point placements.
https://www.meshlab.net – Meshlab, very basic surface model editing and visualisation software.
https://www.blender.org – Blender, extremely advanced surface model editing and visualisation software with a hellish learning curve.
Taxonomy-related tools
https://www.itaxotools.org – iTaxoTools software suite, includes species delimitation, mapping, data cleaning, diagnosis writing, basic statistics, etc.
Reference management
https://www.mendeley.com – Mendeley, a free ref management software
https://www.zotero.org – Zotero, a free ref management software
Reference Navigation
https://www.connectedpapers.com/ – creates a network of citations from papers, helping to find papers you should read
Audio analysis
https://www.audacityteam.org – Audacity, software for visualising, editing, and analysing audio files
Sequence management and analysis
https://ormbunkar.se/aliview – Aliview, for sequence alignment and examination
https://www.megasoftware.net/home – MEGA, for sequence alignment, basic tree building, and ML methods
https://antonellilab.github.io/raxmlGUI – RAxML, for generating phylogenies under Maximum Likelihood (better than MEGA, but more restricted functions)
http://www.iqtree.org/ – IQTree, for generating phylogenies under Maximum Likelihood (arguably more powerful than RAxML)
https://github.com/rambaut/figtree – FigTree, basically the only software out there for visualising phylogenies easily and quickly.
https://github.com/beast-dev/tracer – Tracer, software for examining trace files of Bayesian analyses of all kinds, especially for phylogenetics.
https://beast.community – BEAST and its associated softwares, used for Bayesian Inference phylogenetics and related methods. Quite strong learning curve, but very powerful.
https://nbisweden.github.io/MrBayes/download.html – MrBayes, software for Bayesian Inference phylogenetics. Less complex than BEAST, but also less flexible.
https://usegalaxy.eu – GALAXY, an EU server for doing genomics and other genetics research. Very powerful.
Data management
https://openrefine.org – OpenRefine, software for cleaning up datasets. Very powerful.
Project management
https://airtable.com – AirTable, software for managing projects using relational databases. Free version contains enough functionality for most purposes.
https://www.notion.so – Notion, software for managing notes that can be used to manage projects using relational databases. Very similar functionality to AirTable, but a little less functionality in the free version.
Note taking
https://www.notion.so – Notion, software for managing notes.
https://obsidian.md – Obsidian, software for taking notes and linking between them, a bit like a personal wiki.