GeneGrouper has many parameters so that you can find and group gene clusters of interest more easily. Here are some examples of how to use them.

Examples of different searches with find_regions

• Search for regions to 2,000 bp upstream and 18,000 bp downstream of a seed gene.

GeneGrouper -d /path/to/main_directory -n gene_search \
find_regions \
-f /path/to/query_gene.fasta -us 2000 -ds 18000

• Restrict regions to those containing a seed gene with >=70% identity and >=90% coverage to the query gene.

GeneGrouper -d /path/to/main_directory -n gene_search \
find_regions \
-f /path/to/query_gene.fasta -i 70 -c 90

• Allow for up to one region extracted per genome.

GeneGrouper -d /path/to/main_directory -n gene_search \
find_regions \
-f /path/to/query_gene.fasta -hk 1

• Set the minimum number of gene clusters per group to 3.

GeneGrouper -d /path/to/main_directory -n gene_search \
find_regions \
-f /path/to/query_gene.fasta --min_group_size 3

• Force GeneGrouper to re-write the gene_search folder if it already exists.

GeneGrouper -d /path/to/main_directory -n gene_search \
find_regions \
-f /path/to/query_gene.fasta --force

• Do all the above in one search

GeneGrouper -d /path/to/main_directory -n gene_search \
find_regions \
-f /path/to/query_gene.fasta -us 2000 -ds 18000 -i 70 -c 90 -hk 1 --min_group_size 3 --force

Examples of different group visualizations using visualize

• Save the main visualization in SVG format

GeneGrouper \
-d /path/to/main_directory -n gene_search \
visualize \
--visual_type main \
--image_format svg

• Visualize all subgroups in group label 0

GeneGrouper -d /path/to/main_directory -n gene_search \
visualize \
--visual_type group --group_label 0

• Visualize phylogenetic tree and keep only group labels on the tips. Increase tip label size. Save in SVG format.

GeneGrouper \
-d /path/to/main_directory -n gene_search \
visualize \
--visual_type tree \
--image_format svg \
--tip_label_type group \
--tip_label_size 4