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Project 9: Using CollapseTree with Taxonomic Metadata #9
Large phylogenetic trees with hundreds or even thousands of nodes are impractical to view, and those who need them in their research have limited options for manipulating trees of this size. The collapseTree function in R's phytools package allows users to manually select branches of a phylogenetic tree to collapse, which achieves what the viewer of a large tree might want, but manually selecting the branches becomes difficult for the largest trees, or if the user would like to quickly make a series of different views of the same large input tree. By using taxonomic rank metadata and a stylesheet indicating which taxa should be collapsed, the existing collapseTree function could be used to be used to automate how branches in the tree are collapsed.
For collapseTree, the team will work towards adding the following functionalities:
Hey team lead, we've been gathering Github IDs for your team members. As you've likely been notified, we've created a project repo for you that you are now the admin of and have added the team members to this. We've received almost everyone's Github ID and will continue to add members as we got their Github IDs.
Project repo: https://github.com/hackseq/2017_project_9
Feel free to rename the repo as appropriate. Note that the repo currently has an MIT license. Amend this as required. It'd be a great idea to start a discussion on this repo with information to get your team members started (e.g. some small suggested reading, things to look up, etc). We will also be adding everyone to Slack and creating a specific channel for each project. This may be an easier way to communicate.