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Updated QuickStart EukPhylo (markdown)

Godwin Ani 2025-01-24 16:25:46 -05:00
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QuickStart-EukPhylo.md

@ -25,15 +25,15 @@ Dependencies & third party tools, along with the versions that we use at the Kat
* RAxML (8.2.12) * RAxML (8.2.12)
* BLAST+ (2.9.0) * BLAST+ (2.9.0)
* Vsearch (2.21.1, compiled with GCC 10.3.0) * Vsearch (2.21.1, compiled with GCC 10.3.0)
* Python libraries (can be installed with Pip) * Python (3.9.6, libraries can be installed with Pip)
* ETE3 (pip install ete3) * ETE3 (pip install ete3)
* BioPython * BioPython (1.79-foss-2021b)
* tqdm * tqdm
# EukPhylo part 1 = Assigning Gene families # EukPhylo part 1 = Assigning Gene families
EukPhylo part 1 runs CDS or assembled transcripts through several scripts in order (7 for transcriptomes, 5 for genomes). These scripts are run through a ‘wrapper’ script. EukPhylo part 1 runs CDS (genome) or assembled transcripts (transcriptome) through several scripts in order (5 for CDS, 7 for assembled transcripts). These scripts are run through a ‘wrapper’ script.
## Transcriptomes: ## Transcriptomes:
### Set Up: ### Set Up: