mummer を Homebrew, apt でインストール

プロジェクトリンク

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コマンドとエイリアス

• combineMUMs
• delta-filter
• dnadiff
• exact-tandems
• mummer
• mummerplot
• nucmer
• promer
• repeat-match
• show-aligns
• show-coords
• show-diff
• show-snps
• show-tiling

プロジェクトの歴史

The package's major releases track the growth of genome data. MUMmer 2.1 added NUCmer and PROmer and was described by Delcher, Adam Phillippy, Jane Carlton, and Salzberg as faster and more memory-efficient for large-scale genome alignment and comparison. MUMmer 3.0, described by Stefan Kurtz, Phillippy, Delcher, and collaborators in Genome Biology, made the software open source and better suited to comparing large genomes. MUMmer4, developed by Guillaume Marcais and Aleksey Zimin with the broader MUMmer team, reworked the core from MUMmer3's 32-bit suffix tree constraints toward a 48-bit suffix-array approach and added parallel query processing; the PLOS Computational Biology paper describes MUMmer and nucmer as among the widely used alignment packages in genomics.

使われ方

In practice, researchers use the suite's commands for whole-genome alignment, draft assembly comparison, contig-to-contig alignment, variant and SNP inspection, dot plots, and translated protein-level comparisons. The package-manager niche is scientific command-line software: Homebrew and Debian/Ubuntu packages expose tools such as `mummer`, `nucmer`, `promer`, `dnadiff`, `delta-filter`, `show-coords`, `show-snps`, and `mummerplot`, making a research-grade genome comparison toolkit installable like ordinary Unix utilities.

ソース

• https://academic.oup.com/nar/article/27/11/2369/1258501
• https://formulae.brew.sh/formula/mummer
• https://github.com/mummer4/mummer
• https://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1005944
• https://mummer4.github.io/