Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
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The etetoolkit is a comprehensive toolkit designed for phylogenetic tree manipulation and analysis, addressing the need for researchers in the field of phylogenomics to efficiently analyze and visualize complex tree structures. This skill provides users with the capability to read, write, and modify various tree formats, facilitating a deeper understanding of evolutionary relationships among species. By offering tools for tree manipulation, event detection, and integration with biological databases, etetoolkit empowers researchers to uncover evolutionary patterns and insights critical for their studies.
etetoolkit supports Newick, NHX, PhyloXML, and NeXML formats for reading and writing trees.
Yes, etetoolkit can detect duplication and speciation events, as well as identify orthologs and paralogs based on evolutionary history.
Yes, etetoolkit can integrate with multiple sequence alignments in formats such as FASTA and Phylip.
Researchers and professionals in the fields of phylogenetics, evolutionary biology, and bioinformatics would find etetoolkit particularly useful.
Users need to have the ETE library installed, along with the necessary dependencies for handling tree and alignment files.
Quick Setup:
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davila7/claude-code-templates