I am attempting to create a concatenation-based phylogeny - which requires each of the individually aligned loci to be concatenated into a supermatrix - but I am struggling to find tools available in Galaxy to do this.
Could you please provide some guidance of which tools are available and compaible with IQ-Tree? Alternatively, could tools (e.g., SCaFoS, PHYLUCE, AMAS, SPLACE) be installed so I can complete this step?
Thank you!
I probably misunderstood the topic, but do you mean something similar to MAF blocks? If yes, try Join MAF blocks by Species.
Kind regards,
Igor
I agree with @igor
An example is in the 2012 publication linked in this topic.
The topic also includes a recent example history for a few of the tools, but the full protocol in the publication is still possible (including the multi-species filtering and merging). The only difference is that you will need to supply the reference multi-way conservation data yourself from the history. UCSC is one source.
Any questions, please ask! 