etetoolkit

To visualize phylogenetic trees from Newick files, you can parse the file and render publication-quality figures with customizable styles. This Skill uses the ETE3 library to load Newick formats and export high-resolution images like PNG.

Yes, you can add metadata annotations to nodes and navigate complex tree structures. The Skill supports tree traversal and node annotation, allowing you to mark events like duplications directly within Newick, NHX, or PhyloXML formats.

NCBI taxonomy integration maps species within your phylogenetic tree to their taxonomic lineages. This allows you to perform evolutionary biology and comparative genomics analysis by linking tree leaves to the NCBI taxonomy database.

Supported phylogenetic tree formats include Newick, NHX, and PhyloXML. The Skill parses these formats to facilitate tree manipulation, node annotation, and the generation of publication-quality visualizations for evolutionary biology research.

Yes, PyQt5 is a required dependency for rendering publication-quality phylogenetic tree figures. Alongside numpy and lxml, PyQt5 provides the graphical framework needed by the ETE3 toolkit to generate high-resolution visual outputs.

Analyzing gene family evolution involves loading a Newick tree, annotating nodes with duplication events, and visualizing branch lengths proportional to evolutionary distance. This Skill provides the ETE3 functionality needed to execute this comparative genomics workflow.