The new pipeline experience introduces a streamlined, guided MCScanX workflow presented as a six-step wizard. Users can optionally upload genomes by providing a species name and abbreviation (with built-in availability checks). A PEP file is required, while BED/GFF and CDS files are optional, along with optional image upload and a public visibility toggle. Users can then select betweenuploaded gneomes and genomes available from the PGDD library or their own uploads, and configure DIAMOND and MCScanX parameters, including E-value thresholds, minimum anchors, and maximum gap size. Ka/Ks analysis can be enabled with selectable methods (YN, NG, or MYN) and configurable maximum pair limits. Before execution, the system presents a review page with an estimated runtime. Once submitted, users can monitor progress via a live progress bar and continuously updating pipeline logs (polled every few seconds). Analyses can be resumed at any time using a job-specific resume link. Upon completion, a comprehensive results page is generated, providing immediate access to the multi-synteny viewer, dot plot and riparian visualizations for the primary genome pair, a detailed Ka/Ks report, and downloadable Ks plots. Users can also quickly initiate a new analysis with a one-click reset.