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Dear developers,
When I run `dRep` with the `-nc` parameter set to `0.6`, the program generates most output correctly but the PDF files of the secondary clustering dendrograms and MDS cannot be ope…
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## Motivation
Pangenomes are key to understanding the distribution of gene content and synteny across closely related genomes. Currently, the driving force behind this strategy is sequence alignmen…
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Dear Prof. Barrick,
I regularly use breseq, finding it to be very powerful and valuable tool for my research.
I recently used gdtools PHYLOGENY to get the phylogenetic tree for my clonal samples…
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**Are you using the latest release?**
If you are not using the latest release of funannotate, please upgrade, if bug persists then report here.
**Describe the bug**
A clear and concise descriptio…
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Description of the [problem](https://github.com/CSB5/OPERA-MS/issues/25#issuecomment-1947891847)
1) Question regarding memory: I ran
> /export/opt/sw/opera-ms/0.8.3/OPERA-MS//tools_opera_ms//ma…
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Hi!
I am running ISEScan on a large set of genome assemblies (consisting primarily of assemblies from Illumina data and a couple PacBio genome assemblies). The tools runs great on the test data and m…
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Using a random subset of 21,562 protein signatures from prodigal translation of pigeon1.0 --
1. threshold = 0.1; protein k=7; batch size = 5000;
`time python find-founders.py -k 7 --moltype prot…
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I have questions about options in https://github.com/SionBayliss/PIRATE/blob/master/README.md
## Usage
### Basic examples
- `-a|--align`
- `-r|--rplots`
Running PIRATE with the options `-…
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**Are you using the latest release?**
Yes, version 1.8.16 as installed per https://funannotate.readthedocs.io/en/latest/install.html via conda.
**Describe the bug**
Funannotate train generates a …
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In the clustering process, some groups may have a large number of sequences, which do not have much impact on the whole analysis, but will occupy a large amount of computing resources. Can you set a p…