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

Adri K. Grow 2025-01-28 15:22:00 -05:00
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EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md

@ -20,7 +20,7 @@ The following are required to run EukPhylo part 1. The dependencies are confirme
* [Guidance](https://taux.evolseq.net/guidance/) (version 2.0.2) * [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). * 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). * 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) * [trimAl](https://vicfero.github.io/trimal/index.html) (version 2.rev0)
* [MAFFT](https://mafft.cbrc.jp/alignment/software/) (version 7.49) * [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) * [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)