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Metabolic-Pathway-Presence-Heatmap (MPPH):Constructing phylogenetic trees based on metabolic pathways.

Du, Y.-H.; Mu, J.-H.

2023-06-27 bioinformatics
10.1101/2023.06.27.546232 bioRxiv
Show abstract

Genome sequencing has revolutionized the study of biological systems, enabling exploration of species origins, evolution, and identification. However, traditional methods for constructing phylogenetic trees based on raw sequence data require substantial computational resources and may be challenging for biologists with limited computer knowledge. To address this, a lightweight tree-building tool was developed, Metabolic-Pathway-Presence-Heatmap (MPPH), leveraging Python programming and the KEGG metabolomics database to construct phylogenetic trees based on metabolic pathway information. This approach reduces computational and time requirements while focusing the analysis on metabolic pathways. The tool provides a rapid and reliable option for biologists to investigate the evolutionary and taxonomic aspects of species. Additionally, the tool incorporates a heatmap feature, allowing users to visualize the presence or absence of metabolic pathways across multiple species. The code is available at http://github.com/DeweyYihengDu/Metabolic-Pathway-Presence-Heatmap.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.