I have just released the latest version of the Visual Genome Browser. This new version contains Read Mapping from CRAM files, visualization of VCF files and full pairwise alignment with Minimap2, LastZ as well as tBlastx into a easily navigable 2D Dot Plot. Feel free to download the latest version and start experimenting and validating genomic findings from publications for yourself.
You can compare entire organisms' genomes by starting with the Overlay Mapping which uses Kmer-db to find the matching chromosomes. You can then calculate the Minimap2 alignment between each of the chromosome pairs and even use the annotation data from both genomes to do a brute force protein level pairwise alignment search, starting with a blazingly fast .Net implementation of the Myers's bit-vector algorithm, which is then followed by more precise pairwise alignments using Blosum matrices. It is free and utilizes various tools such as Samtools and Blast to make this all possible. A visual GUI bringing together numerous bio-informatics tools as well as 10 years of C# development effort.

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