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

Katzlab 2025-02-13 15:31:06 -05:00
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EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md

@ -9,7 +9,7 @@ EukPhylo part 2 starts from the “ReadyToGo” files produced by part 1 (or any
Example output files for EukPhylo part 2 and the contamination loop can be found [here](https://doi.org/10.6084/m9.figshare.26662018.v1).
# Set Up
# Install (only need to do once)
## Dependencies
The following are required to run EukPhylo part 1. The dependencies are confirmed to work using the version numbers in parentheses, though other versions may work as well.
@ -24,6 +24,8 @@ The following are required to run EukPhylo part 1. The dependencies are confirme
* [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)
# Setup
## Input data and folder structure
Running EukPhylo Part 2 requires at least four items in your main directory:
@ -31,6 +33,8 @@ Running EukPhylo Part 2 requires at least four items in your main directory:
* A folder containing your input files
* A taxon list
* An OG list
* An Output folder
* a shell script (or equivalent) to load modules and run programs ++
See below for details.