ksrates
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VIB-PSB
ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-ortholog Ks distributions.
Hi, I'm using the ksrates docker image. I have an issue with not getting relevant output files. Here are the codes I have run, ``` /usr/local/bin/ksrates init config_oxalis.txt /usr/local/bin/ksrates paralogs-ks...
- Version lock i-ADHoRe to release 3.1 - Update syntax in push_container.yml
Hi Cecilia, This looks like a great application! I have a few questions: 1) Does the Ksrates output provide the equation and/or lognorm fit parameters for the mixture-model fits? I'd...
This PR makes the Nextflow pipeline file (`main.nf`) in `ksrates` compatible with the recent [Nextflow DSL2 syntax](https://www.nextflow.io/docs/latest/dsl2.html), which has replaced the older DSL1 since version `22.03.0-edge`. Based on my experience,...
Hello, Thank you for making this tool. It have been useful for a few research projects already. Does ksrates remove paralogous ks anchor pair data smaller than 0.05? If so,...
**Generate Ks plots using bottom-ranked reciprocally retained gene families** This PR adds the possibility to run the reciprocal retention Ks pipeline for the _bottom_-ranked GFs instead of the _top_-ranked GFs....
Command `paralogs-ks-multi` throws an error: ``` ksrates paralogs-ks-multi config_files/config_myspecies.txt TypeError: wgd_paralogs() missing 1 required positional argument: 'test' ``` **Cause** The click command [calls](https://github.com/VIB-PSB/ksrates/blob/23690e6f820249026e17ab41f6e33a64245c110e/ksrates_cli.py#L348) `wgd_paralogs()` through: ``` wgd_paralogs(source, expert, n_threads, custom_recret_gfs,...
ksrates uses **paml4.9j** from [http://abacus.gene.ucl.ac.uk/software/paml4.9j.tgz](http://abacus.gene.ucl.ac.uk/software/paml4.9j.tgz), which is not available to date (08/08/2025) because the website is down. This means that installation of ksrates can't be completed and that the CI...