Software and resources

Software

These links are provided for information only, they are not needed now for the practical but if you finish any exercises early you may want to investigate the tools/resources a little further by checking out their websites, user guides, and/or their main publications.

BUSCO - Benchmarking Universal Single-Copy Orthologues

CAFE - computational analysis of gene family evolution

iTOL - online phylogenetic tree viewer

JalView: for multiple sequence alignment editing, visualisation and analysis

MAFFT - multiple sequence alignment tool

OrthoDB - orthology database

RAxML - maximum likelihood phylogenies

Treerecs - tree reconciliation software

TrimAl - alignment filtering tool

R and packages

R

Website
There are no publication for R itself but you should still cite it
Userguide

Chronos function of the ape package

Folder with intermediate result files

If you get stuck, you can find all intermediate results files in the virtual gitpod workspace /workspace/biodivinfo/data/. Simply fetch the correct output files in order to continue with the next steps of the practical:

Use the copy cp command from the terminal in gitpod, e.g.:
cp /workspace/biodivinfo/data/the_file_you_want_to_copy path/to/destination/
If the files are zipped (i.e. if the name ends with .zip), you can uncompress them with:
unzip /path/to/file.zip