Evolutionary Genomics — Analyses, Queries & Utilities

• Refer, as well, to the Comparative Genomics category.



• Best matches
  • listing each ORF's top BLASTP matches.
  • finding ORFs matching genes from one set of genomes better than another set of genomes.


• Distribution of ORFs across lineages:
  • finding lineage- or species-specific ORFs.
  • finding ubiquitously distributed ORFs.
  • finding ORFs that are in most members of every prokaryotic phylum.
  • listing consensus gene names that are ubiquitously distributed.
  • finding ORFs present in subsets of lineages.
  • finding ORFs whose best match is to a specified lineage.


• Genome-level phylogenetics:
  • producing a distance matrix based on normalized BLASTP similarity or on the proportion of shared inventory.


• Gene-level phylogenetics:
  • finding possible events of lateral gene transfer or reciprocal paralog loss using four-taxon tree analysis or simple similarity searching.
  • producing a distance matrix based on normalized BLASTP similarity.
  • retrieving sequences in multiple FASTA-format.

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