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

Katzlab 2025-02-13 15:34:30 -05:00
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EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md

@ -11,8 +11,7 @@ Example output files for EukPhylo part 2 and the contamination loop can be found
# Installation # Installation
## Dependencies The following dependencies are required to run EukPhylo part 2, and only needs to be done once. The dependencies are confirmed to work using the version numbers in parentheses, though other versions may work as well.
The following are required to run EukPhylo part 1, and only needs to be done once. The dependencies are confirmed to work using the version numbers in parentheses, though other versions may work as well.
* Python 3, and the following libraries: * Python 3, and the following libraries:
* [Biopython](https://biopython.org/docs/latest/index.html) (version 1.75) * [Biopython](https://biopython.org/docs/latest/index.html) (version 1.75)
* [ETE3](http://etetoolkit.org/) (version 3.1.2.) * [ETE3](http://etetoolkit.org/) (version 3.1.2.)