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When importing (unrooted) phylogenies, the current phyloseq tutorials and/or functions implement a very ad hoc rooting of the tree, placing the root at a randomly picked tip, like so:
``` R
tree.root…
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**Authors:** Fiona C. Wood, Yonas I. Tekle
**Abstract:** The advent of molecular phylogenetics has led to numerous cases where species determination differs based on molecular or morphological data. …
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Following our discussion with @nekrut , I am creating an issue to outline essential components for creating a barebones HIV (or other short RNA virus) genomic analysis pipeline.
Key steps for ampl…
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This has multiple aspects:
- The phylogenetic tree needs to be displayed. Probably its own display page on the same level as the alignment display. Should leverage existing tools for displaying phy…
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The Bioperl mailing lists (as well as all other OBF mail lists) had been having serious issues over the last several months due to heavy spam traffic on the OBF mailman server. I am soliciting commun…
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I am not able to connect to the postgres DB below. I have changed/set the password to match the value in ./Airavata_Remote_Job_Runner/WebContent/WEB-INF/spring/application_servlets/applicationContext.…
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Hello again! It looks like the S3 download fasta and metadata files have not been updated in a bit over a week -- does something need a restart?
```
curl -s -I https://cog-uk.s3.climb.ac.uk/phyloge…
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- [x] Download the Genome from NCBI
GCF_000767585.1_PRJNA234474_Ca_dromedarius_V1.0_genomic.fna.gz`
### LTR-Detection
- [x] **Create index** _find pairs of maximal exact direct repeats that a…
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@dpbisme suggested possibly filtering nodes by degree for ex, or centrality
i assume this is by user control
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Hello,
I am facing errors using mp-est 2.0, at the compilation step .
I am running on the platform of linux, First I instlall mp-est 2.0 by git clone https://github.com/lliu1871/mp-est.git, and …