Comparative Genomics of Ten New Caenorhabditis Species with Phylogenomic Analysis

1988 single-copy loci from 27 Caenorhabditis species form a supermatrix for phylogenomic analysis. The dataset includes multiple species tree files generated by ASTRAL-III, RAxML, and PhyloBayes, along with orthology clustering and gene structure statistics. Lewis Stevens from the University of Edinburgh created this dataset for comparative genomics research.

Use Cases

• Reconstructing species phylogenies based on the provided ASTRAL-III and RAxML tree files.
• Analyzing orthologous gene groups across Caenorhabditis species using the Orthogroups.txt file.
• Studying gene structure and genome size variation using the genome_gene_structure_stats.tsv file.
• Investigating the evolution of specific protein families, such as Notch-like receptors, using the provided FASTA alignments and trees.

Strengths

• Includes a supermatrix of 1988 single-copy loci for phylogenomic analysis.
• Provides multiple species tree estimates from different methods (ASTRAL-III, RAxML, PhyloBayes) for comparison.
• Contains specific analysis files for a Notch-like receptor orthogroup, including alignments and phylogenetic trees.

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

University of Edinburgh

Collection Method

Phylogenomic analysis of genomic data, likely from sequencing.