ITOL Link to Single-Gene Trees of Nucleus-Encoded Plastid-Targeted Genes

A collection of 1,670 single-gene phylogenetic trees for nucleus-encoded plastid-targeted genes in complex algae, created by Mick Van Vlierberghe and last updated on 2026-05-24. The trees were inferred from 1,788 plastid-related orthoclans extracted from 31,784 photosynthetic clans, derived from 73 curated eukaryotic proteomes enriched with 172 MMETSP transcriptomes. Inference used IQ-TREE under the LG4X model with 1,000 ultrafast bootstrap replicates.

Use Cases

• Inferring plastid-related gene transfer events based on the PAGTI pipeline input described.
• Studying orthology and gene family evolution based on the described OrthoFinder-derived orthoclans.
• Analyzing phylogenetic relationships of plastid-targeted genes across eukaryotic lineages based on the taxon sampling described.

Strengths

• Contains 1,670 single-gene trees with detailed inference methodology described.
• Derived from a substantial base of 73 curated eukaryotic proteomes and enriched with 172 transcriptomes.
• Trees were generated with 1,000 ultrafast bootstrap replicates for alignments with 4 or more sequences.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• The dataset size is listed as 0.0 B, indicating a very limited scope or a metadata placeholder.

Provenance

Source

Mick Van Vlierberghe via figshare.

Collection Method

Trees inferred with IQ-TREE from OrthoFinder-derived orthoclans, enriched with MMETSP transcriptomes using Forty-Two.

Freshness

Last updated 2026-05-24 15:29:26; freshness should be verified.