Kssdtree is a versatile Python package for phylogenetic analysis, offering three distinct pipelines: the Routine Pipeline, the Reference Subtraction Pipeline, and the GTDB-based Phylogenetic Placement Pipeline.
Routine Pipeline: A general-purpose tool for phylogenetic analysis of user genomic data. Reference Subtraction Pipeline: Designed for population-level phylogenetic analysis. GTDB-based Phylogenetic Placement Pipeline: Facilitates the search for similar genomes in the Genome Taxonomy Database (GTDB), conducting phylogenetic analysis alongside these genomes and positioning the input genomes within the entire prokaryotic tree of life. Kssdtree also provides one-stop tree construction and visualization. It can handle DNA sequences in both fasta and fastq formats, whether gzipped or not. Additionally, Kssdtree is compatible with multiple platforms (Linux, MacOS, and Windows) and can be run using Jupyter notebooks.
More usages about Kssdtree, please see Kssdtree documentation (https://kssdtree.readthedocs.io/en/latest).