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Aligning multiple whole genomes with Mercator and MAVID.
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MAVID multiple alignment server.
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MAVID: constrained ancestral alignment of multiple sequences.
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Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data.
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Base-By-Base: single nucleotide-level analysis of whole viral genome alignments.
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VISTA family of computational tools for comparative analysis of DNA sequences and whole genomes.
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An introduction to the Lagan alignment toolkit.
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Strategies and tools for whole-genome alignments.
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seq-seq-pan: building a computational pan-genome data structure on whole genome alignment.
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PLATCOM: a Platform for Computational Comparative Genomics.
Bioinformatics. 2005 May 15;21(10):2514-6. doi: 10.1093/bioinformatics/bti350. Epub 2005 Feb 24.

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3D genome evolution and reorganization in the Drosophila melanogaster species group.
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Draft genomes of two outcrossing wild rice, and , reveal genomic features associated with mating-system evolution.
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Comparative Genomic Characterization of the Multimammate Mouse Mastomys coucha.
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