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Updated QuickStart EukPhylo (markdown)
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# EukPhylo part 1 = Assigning Gene families
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EukPhylo part 1 runs CDS (genome) or assembled transcripts (transcriptome) through several scripts in order (5 for CDS, 7 for assembled transcripts) to produce ReadyToGo files. These scripts are run through a ‘wrapper’ script.
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EukPhylo part 1 runs CDS (genome) or assembled transcripts (transcriptome) through several scripts in order (5 for CDS, 7 for assembled transcripts) to remove bacterial contamination and produce ReadyToGo files. These scripts are run through a ‘wrapper’ script.
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## Transcriptomes:
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### Set Up:
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