Phylogenetic and Phytochemistry Data for Plant-Parasitoid Cophylogeny Study

Ryan D. Ridenbaugh provides alignment files, R scripts, and input data for phylogenetic and phytochemical analyses. The dataset includes FASTA and Nexus files for Bayesian and maximum likelihood phylogenies, plus input files for Jane 4 and PACo cophylogenetic analyses. An R script and input files are included for PCA and Random Forest analyses of plant phytochemistry.

Use Cases

• Inferring phylogenetic trees based on sequence alignments provided in FASTA and Nexus formats.
• Performing cophylogenetic analyses using the provided Jane 4 and PACo input files.
• Analyzing plant phytochemistry data through Principal Component Analysis (PCA) using the included R script.
• Building predictive models of phytochemical influence using Random Forest analysis with the provided input files.

Strengths

• Includes multiple analysis-ready file types: FASTA, Nexus, and R script inputs.
• Supports several established phylogenetic methods: Bayesian inference, maximum likelihood, and cophylogenetic analysis.
• Provides scripts for both ordination (PCA) and machine learning (Random Forest) analyses.

Limitations

• Row count and dataset scale are unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• Description metadata is limited; actual data quality requires manual inspection after download.

Provenance

Source

Ryan D. Ridenbaugh via paperswithcode

Collection Method

Likely compiled for the research paper 'Plant Phytochemistry Influences the Niche Breadth of Oligophagous Parasitoids (Hymenoptera: Braconidae)'.