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Updated EukPhylo QuickStart (markdown)

Godwin Ani 2025-02-27 18:15:54 -05:00
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EukPhylo-QuickStart.md

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> Note: The EukPhylo pipeline is currently being dockerised for easier installation and use. More information about the dockerfile can be found here - [Docker branch](https://github.com/Katzlab/EukPhylo/tree/Docker)
# General Steps # General Steps
EukPhylo pipeline is composed of two parts, that can be run individually: Part 1 can be run only once, to assign gene families; Part 2 builds MSAs, trees, and implements contamination removal and concatenation. It's preferable to run Part 2 using the outputs of Part 1 as input, but this is not required as long as the input files are in the same format (one fasta file per species, with sequences IDs starting with a 10 digit taxon identifier and ending in a gene family identifier with the format OGx_xxxxxx. See extended version of the wiki for details.) EukPhylo pipeline is composed of two parts, that can be run individually: Part 1 can be run only once, to assign gene families; Part 2 builds MSAs, trees, and implements contamination removal and concatenation. It's preferable to run Part 2 using the outputs of Part 1 as input, but this is not required as long as the input files are in the same format (one fasta file per species, with sequences IDs starting with a 10 digit taxon identifier and ending in a gene family identifier with the format OGx_xxxxxx. See extended version of the wiki for details.)