From 9114c8b6adf9091b0ae9e12eac95eaf6593e51bc Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Wed, 22 Jan 2025 13:09:51 -0500 Subject: [PATCH] Updated EukPhylo Part 2: MSAs, trees, and contamination loop (markdown) --- EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md b/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md index b7692c7..8b02eb8 100644 --- a/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md +++ b/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