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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). 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 ## 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. 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) * [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)
# Setup
## Input data and folder structure ## Input data and folder structure
Running EukPhylo Part 2 requires at least four items in your main directory: 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 folder containing your input files
* A taxon list * A taxon list
* An OG list * An OG list
* An Output folder
* a shell script (or equivalent) to load modules and run programs ++
See below for details. See below for details.