-
Hi,
I am trying to plot synteny between 5 genomes. I have calculated pairwise synteny blocks as follows:
Ref genome species 1
species 1 species 2
species 2 species 3
species 3 species 4
I …
-
Hi,
Thanks for the wonderful package, it's a lot easier to use than most of the synteny block detection and plotting pipelines. I'm curious if there's a built-in way to run the BLAST+ command with mu…
-
As long as we are on a synteny kick, circular displays are a popular way to visualize synteny. This would have two genomes on different sides of the circle
-
Greetings I'm a PhD student, working on visualization of synteny across genomes of strains of the same species (12 different synteny plots), and one synteny across different species genomes (up to 35 …
-
Could you please elaborate on the -b parameter usage?
`-b block_sizes comma-separated list of synteny block scales [default = 5000]
`
What is a synteny block scale and how to find an optimal one fo…
-
In olden days, we had options in the macro view for "micro-synteny ordering" and "micro-synteny only" (filtering). These are not yet available in GCV2.0. Bring 'em back!
-
The micro-synteny viewer is great at visualizing the similarities and differences between gene family tracks. However, when there are many results tracks, it's hard to visually compare tracks that are…
-
Currently the red (plus yellow/blue for insertion/deletion) are hardcoded in the LinearSyntenyRendering
Add ability to use custom methods
From pairing with @garrettjstevens
-
Importing dependencies
Run name: get_synteny
Accessions: ['GCA_914767715.1', 'GCF_902652985.1']
No alg species provided. Tracing groups from chromosomes of first species listed: GCA_914767715.1
No…
-
Hi @rhysf,
First of all, thank you very much for this awesome tool. I have some results from the Synteny output which is confusing for me. I would be grateful to you if you can answer them.
I have…