Student Resources


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.netMeshlab, very basic surface model editing and visualisation software.

https://www.blender.orgBlender, extremely advanced surface model editing and visualisation software with a hellish learning curve.


Taxonomy-related tools

https://www.itaxotools.orgiTaxoTools software suite, includes species delimitation, mapping, data cleaning, diagnosis writing, basic statistics, etc. 


Reference management

https://www.mendeley.comMendeley, a free ref management software

https://www.zotero.orgZotero, 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.orgAudacity, software for visualising, editing, and analysing audio files


Sequence management and analysis

https://ormbunkar.se/aliviewAliview, for sequence alignment and examination

https://www.megasoftware.net/homeMEGA, for sequence alignment, basic tree building, and ML methods

https://antonellilab.github.io/raxmlGUIRAxML, 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/figtreeFigTree, basically the only software out there for visualising phylogenies easily and quickly.

https://github.com/beast-dev/tracerTracer, software for examining trace files of Bayesian analyses of all kinds, especially for phylogenetics.

https://beast.communityBEAST 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.htmlMrBayes, software for Bayesian Inference phylogenetics. Less complex than BEAST, but also less flexible.

https://usegalaxy.euGALAXY, an EU server for doing genomics and other genetics research. Very powerful.


Data management

https://openrefine.orgOpenRefine, software for cleaning up datasets. Very powerful.


Project management

https://airtable.comAirTable, software for managing projects using relational databases. Free version contains enough functionality for most purposes.

https://www.notion.soNotion, 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.mdObsidian, software for taking notes and linking between them, a bit like a personal wiki.