Phyloboost is a python pipeline that allows the reconstruction, augmentation and visualizaton of the similarity-cluster-based tree sets constructed from an input dataset of sequences. The end point is a data object that can be explored or used to quantify the phylogenetic signal present in whatever dataset acted as the input. While originally developed as a tool to allow the synthesis and calculation of the phylogenetic signal in Genbank for Eukaryotes, it will work on any large set of DNA or RNA sequence data.
- Build denovo clusters based on genetic similarity.
- Filter the clusters removing taxonomically mislabled sequences, transposons, and model organisms.
- Build alignments for all of the cluster sets.
- Build unrooted trees for all of those alignments.
- Extract a set of rooted convex subtrees from the unrooted tree set.
- Merge all rooted trees into a common data structure, allowing you to compare and visualize those trees aligned to the NCBI taxonomy.
$ git clone https://github.com/lcoghill/phyloboost
$ cd /phyloboost
Authors and Contributors
Support or Contact
Having trouble? Check out the documentation at Phyloboost Wiki or contact @lcoghill and we’ll help you sort it out.