This program helps you extract synteny patterns from a group of similar loci or genomes. This is accomplished by deconstructing contigs into Ngrams (group of neighboring genes of which N is the number of genes) using a sliding window method. Once completed, anvi'o will export a table with Ngrams for you to work with. If more than one annotation source is provided, please designate which annotation_source anvio should use to make the Ngrams with using the –ngram-source parameter (e.g. gene_clusters, COG_FUNCTION). By default anvi'o will ignore Ngrams that contain genes without annotations. If you would like to override this, you can use the –analyze-unknown-functions flag..
Requires or uses
No one has described the usage of this program :/ If you would like to contribute, please see previous examples here, and feel free to add a Markdown formatted file in that directory named “anvi-analyze-synteny.md”. For a template, you can use the markdown file for
anvi-gen-contigs-database. THANK YOU!
Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the
__resources__ tag in this file to see an example.