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Description

Phyloboost is a python pipeline that allows the reconstruction, augmentation and visualizaton of the similarity-cluster-based tree sets constructed from the Phylota pipeline. These trees are unrooted trees built from datasets encompassing all of eukaryota from Genbank with more than 60,000 genera.

Purpose

• Reconstruct the original cluster sets in FASTA format for easy use.
• Augment / Expand the clusters with additional sequences through BLAST searches.
• Filter the clusters removing taxonomically mislabled sequences.
• Filter the clusters removing any 'known' tranposable elements.
• Build alignments for all of the cluster sets.
• Build unrooted trees for all of those alignments.
• Attempt to root those trees via convex subtree graph methods developed by Rick Ree.
• Compare and visualize those trees aligned to the NCBI taxonomy.

Installation

• Install the software requirements
• Install the needed databases
• Prime the databases
• Clone the Phyloboost Repo
• Run the pipeline