TreeTools: Functions for Phylogenetic Tree Creation, Modification, and Analysis

Efficient implementations of functions for the creation, modification, and analysis of phylogenetic trees. The package includes applications for tree generation, rearrangement, shape analysis, rooting, and support calculation, referencing multiple peer-reviewed publications. It is authored by Martin R. Smith and sourced from the paperswithcode platform.

Use Cases

• Generate phylogenetic trees with specified shapes based on described generation functions.
• Analyze tree balance and shape using referenced metrics like 'stemwardness' and tree balance calculations.
• Root trees and extract subtrees for focused evolutionary analysis.
• Calculate and depict split support to assess phylogenetic signal.
• Import and export trees from Newick, Nexus, and TNT formats for interoperability with other tools.

Strengths

• Implementation references multiple peer-reviewed publications, including Klopfstein & Spasojevic (2019) and Asher & Smith (2022).
• Description lists specific applications like tree rearrangement, rooting, and artificial extinction.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Last update date is unknown; freshness unverified.

Provenance

Source

paperswithcode

Collection Method

Likely a software package for phylogenetic analysis.

Time Range

Temporal coverage is unknown.

Freshness

Last updated date is unknown.

Geography

Spatial coverage is unknown.