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## PhyloToL Part I = determining gene families
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## PhyloToL Part I = determining gene families
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### Overview
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### Overview
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### ## Set up
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###Set up
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### ## The hook - for determining gene families
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###The hook - for determining gene families
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### ## Processing transcriptomes
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###Processing transcriptomes
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### ## Processing genomes with CDs
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###Processing genomes with CDs
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### ## Starting at different points in the process (Folder structure)
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###Starting at different points in the process (Folder structure)
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### ## Appendices
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###Appendices
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##PhyloToL Part 2 = generating MSAs and gene trees
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##PhyloToL Part 2 = generating MSAs and gene trees
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###Overview of the process
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###Overview of the process
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