Nematode Phylogenomic Analysis Files and Scripts

Supplementary data for a phylogenomic study of the phylum Nematoda, comparing molecular and morphological classifications. The 3.8 GB collection contains processed files and scripts from a multi-stage bioinformatics pipeline, including ortholog alignments and phylogenetic trees. The data was authored by Mohammed Ahmed and published on figshare in April 2026.

Use Cases

• Compare phylogenetic trees from IQ-TREE and RAxML analyses on the supermatrix file to assess topological robustness.
• Use the ASTRAL species tree output to analyze relationships among nematode clades like TRICHINELLIDA and RHABDITINA.
• Apply the provided SCRIPT to replicate the full analysis pipeline from orthology inference to tree building.
• Analyze the cleaned alignments in the 06_ALICUT folder for specific orthogroups to study sequence evolution.
• Use the proteome files in 01_INPUT for comparative genomics studies within the Nematoda phylum.

Strengths

• Contains outputs from 12 distinct stages of a phylogenomic pipeline, providing a complete workflow trace.
• Data is structured into five major nematode clade datasets (e.g., TRICHINELLIDA, SPIRURINA) for focused analysis.
• Includes the full analysis SCRIPT, enabling reproducibility of the published study.

Limitations

• The dataset is 3.8 GB of processed intermediate files; raw sequence data is not directly included.
• Sample size or number of taxa per clade is not specified in the provided description.
• The description focuses on file structure, with no details on specific metrics like bootstrap support values or alignment statistics.

Provenance

Source

figshare, supplementary data for a manuscript.

Collection Method

Generated through a bioinformatics pipeline including proteinortho, MAFFT, IQ-TREE, RAxML, and ASTRAL.

Freshness

Last updated in April 2026.