clinker
clinker copied to clipboard
gamcil
Gene cluster comparison figure generator
Great job with a tool, it's very nice and handy! Would you consider adding an option to show gene labels just for genes that actually created clusters? In case of...
First off, Wow! well done @gamcil, well done. I've went over so many tools and packages and what not lately to try and generate such figures and clinker is by...
Thank you for developing such a great tool. I have a fasta file and a gff file that I want to use as input for clinker. However, I got the...
Sometimes, it is useful to be able to differentiate between different clades or orthologous groups within a tandem array of homologous genes. See the example below, where a tandem array...
Currently, colors indicating cluster groups represent a rainbow gradient across the loci. Consequently, when analyzing large gene clusters, neighboring genes have very similar colors. This can make it difficult to...
It seems clinker does not work as intended when multi-exon genes are annotated with separate CDS instead of with join(). When this is the case, CDS exons are considered separately...
``` -> % clinker examples/*.gbk -p plot.html [15:29:13] INFO - Starting clinker [15:29:13] INFO - Parsing files: [15:29:13] INFO - A.alliaceusCBS536.65.gbk [15:29:13] INFO - A.burnettiiMST-FP2249.gbk /dat1/nbt2/miniconda3/envs/clinker/lib/python3.12/site-packages/Bio/Seq.py:2880: BiopythonWarning: Partial codon, len(sequence)...
Hello, I am attempting to colour and group sections of a large pESI plasmid. I have 7 different groups along the plasmid backbone and have grouped all of these genes...
The output of the `-mo` option always creates a file in which the first two columns and rows are 0.0. You can verify this by trying different combinations of the...
I would like to understand the specific implications of the results obtained through the '-mo' parameter. The CSV file exported using the '-mo' parameter uses the full gene name as...
