SeqKit2 has significantly expanded its capabilities, doubling the number of subcommands from 19 to 38, and adding support for three more compression file formats. This enhances its versatility and efficiency in sequence and alignment processing. Benchmarking results demonstrate that SeqKit2 consistently outperforms its predecessor and remains competitive with other similar tools. In addition, SeqKit2 has notably improved user-friendliness with the introduction of new features, such as autocompletion for subcommands and command-line flags and enhanced error-handling mechanisms.

The use of Venn diagrams greatly aids in illustrating and visualizing set relationships within metabolomics, genomics, transcriptomics, and proteomics. Here, we introduce EVenn, an all-encompassing platform that provides a unified interface for a wide range of Venn diagram functionalities. This protocol delineates the features of EVenn, encompassing interactive Venn diagrams, interactive Edwards diagrams, Euler diagrams, UpSet plots, flower plots, and Venn network diagrams, solidifying its role as an invaluable tool for the analysis of multiomics data.

Robinia pseudoacacia strategically recruited arbuscular mycorrhizal (AM) fungi to cope with phosphorus limitation. AM fungi interacted with the assembly and composition of bacteria and rhizobia. AM fungal-centered underground network supported slope multifunctionality. The R. pseudoacacia–AM fungi–rhizobia association restores eroded ecosystems.

Bacmethy tool provides a one-stop analysis and visualization pipeline for effectively characterizing bacterial DNA methylation modification features and predicting the regulation patterns. Bacmethy offers both a local run function and an online interface analysis service, providing significant convenience for researchers without coding abilities. Bacmethy provides useful information for decoding the underlying molecular mechanisms of how DNA methylation regulates bacterial cellular and physiological functions.

Fastp is a widely adopted tool for FASTQ data preprocessing and quality control. It is ultrafast and versatile and can perform adapter removal, global or quality trimming, read filtering, unique molecular identifier processing, base correction, and many other actions within a single pass of data scanning. Fastp has been reconstructed and upgraded with some new features. Compared to fastp 0.20.0, the new fastp 0.23.2 is even 80% faster.

Representative visualization results of ImageGP. ImageGP supports 16 types of images and four types of online analysis with up to 26 parameters for customization. ImageGP also contains specialized plots like volcano plot, functional enrichment plot for most omics-data analysis, and other 4 specialized functions for microbiome analysis. Since 2017, ImageGP has been running for nearly 5 years and serving 336,951 visits from all over the world. Together, ImageGP (http://www.ehbio.com/ImageGP/) is an effective and efficient tool for experimental researchers to comprehensively visualize and interpret data generated from wet-lab and dry-lab.

The ggtree object is designed to store phylogenetic tree and associated data, and the object itself is a graphic object that can be rendered as an image file. This work will increase the reproducibility and reusability of phylogenetic data, as well as facilitate integrative and comparative studies.

A new release of PhyloSuite, capable of conducting tree-based analyses. Detailed guidelines for each step of phylogenetic and tree-based analyses, following the “What? Why? and How?” structure. This protocol will help beginners learn how to conduct multilocus phylogenetic analyses and help experienced scientists improve their efficiency.