AbstractSummaryGenome sequences constitute the primary evidence on the origin and spread of the 2019-2020 Covid-19 pandemic. Rapid comparative analysis of coronavirus SARS-CoV-2 genomes is critical for disease control, outbreak forecasting, and developing clinical interventions. CoV Genome Tracker is a web portal dedicated to trace Covid-19 outbreaks in real time using a haplotype network, an accurate and scalable representation of genomic changes in a rapidly evolving population. We resolve the direction of mutations by using a bat-associated genome as outgroup. At a broader evolutionary time scale, a companion browser provides gene-by-gene and codon-by-codon evolutionary rates to facilitate the search for molecular targets of clinical interventions.Availability and ImplementationCoV Genome Tracker is publicly available athttp://cov.genometracker.organd updated weekly with the data downloaded from GISAID (http://gisaid.org). The website is implemented with a custom JavaScript script based on jQuery (https://jquery.com) and D3-force (https://github.com/d3/d3-force).Contactweigang@genectr.hunter.cuny.edu, City University of New York, Hunter CollegeSupplementary InformationAll supporting scripts developed in JavaScript, Python, BASH, and PERL programming languages are available as Open Source at the GitHub repositoryhttps://github.com/weigangq/cov-browser.