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Updated EukPhylo Part 2: MSAs, trees, and contamination loop (markdown)

Auden Cote-L'Heureux 2025-01-22 13:09:51 -05:00
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EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md

@ -19,6 +19,7 @@ The following are required to run EukPhylo part 1. The dependencies are confirme
* [tqdm](https://tqdm.github.io/) (version 4.66.4; unlikely to matter)
* [Guidance](https://taux.evolseq.net/guidance/) (version 2.0.2)
* Note that once you have downloaded Guidance, you will likely have to run the command [chmod u+x](https://www.computerhope.com/unix/uchmod.htm) on the guidance executable script (found within the www folder) as well as all dependency executable scripts (found within the programs folder).
* Both the Guidance AND TrimAL folders as downloaded from the respective websites (see TrimAL link below) should be placed in the Scripts folder (see more info on folder structure below).
* [TrimAL](https://vicfero.github.io/trimal/index.html) (version 2.rev0)
* [MAFFT](https://mafft.cbrc.jp/alignment/software/) (version 7.49)
* [IQ-Tree](http://www.iqtree.org/) (version 2.1.2) and/OR [RAxML](https://cme.h-its.org/exelixis/web/software/raxml/) (version 8.2.12) and/OR [FastTree](https://microbesonline.org/fasttree/) (version 2.1)
@ -26,7 +27,7 @@ The following are required to run EukPhylo part 1. The dependencies are confirme
## Input data and folder structure
Running EukPhylo Part 2 requires at least four items in your main directory:
* A folder named [Scripts](https://github.com/Katzlab/EukPhylo/tree/main/PTL2/Scripts) and containing all scripts from EukPhylo part 2
* A folder named [Scripts](https://github.com/Katzlab/EukPhylo/tree/main/PTL2/Scripts) and containing all scripts from EukPhylo part 2, as well as the Guidance and TrimAL folders downloaded from the respective websites (see links in Dependencies section above).
* A folder containing your input files
* A taxon list
* An OG list