cct
visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
Command lineScience
Not tested on a device yet. What that means
Commands in the package
build_blast_atlasbuild_blast_atlas_all_vs_allbuild_cog_dbcgview_comparison_toolcheck_envconvert_vcf_to_featurescreate_zoomed_mapsfetch_all_refseq_bacterial_genomesfetch_all_refseq_chloroplast_genomesfetch_all_refseq_mitochondrial_genomesfetch_genome_by_accessionfetch_refseq_bacterial_genomes_by_namencbi_searchprocess_sample_projectsprocess_test_projectsredraw_mapsremove_long_seqsremove_short_seqs
About cct
From Debian's package description
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences of interest to existing genomes or sequence collections. The comparisons are conducted using BLAST, and the BLAST results are presented in the form of graphical maps that can also show sequence features, gene and protein names, COG category assignments, and sequence composition characteristics. CCT can generate maps in a variety of sizes, including 400 Megapixel maps suitable for posters. Comparisons can be conducted within a particular species or genus, or all available genomes can be used. The entire map creation process, from downloading sequences to redrawing zoomed maps, can be completed easily using scripts included with the CCT. User-defined features or analysis results can be included on maps, and maps can be extensively customized. To simplify program setup, a CCT virtual machine that includes all dependencies preinstalled is available. Detailed tutorials illustrating the use of CCT are included with the CCT documentation.
From Debian's description of the cct package, under that package's license.
Dependencies
Depends on
perlbioperlcgviewncbi-blast+-legacyimagemagickorgraphicsmagickliberror-perllibtie-ixhash-perllibwww-perl
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Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the cct package, under that package's license.
- Description: Debian's description of the cct package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.