-
Hi,
I randomly sampled a subset of 16s RRNA sequences from the reference sequence fasta file (https://github.com/picrust/picrust2/tree/master/picrust2/default_files/prokaryotic)
/pro_ref/pro_ref.f…
-
@hyanwong noticed that some sequences have the same GenBank accession in the latest Viridian trees.
For example, the following GenBank accessions have multiple sequences associated with them (the l…
szhan updated
17 hours ago
-
Alex noticed this issue and I tested it quickly again today. When I selected a directory for supplementary data for the phylo module (with renamed fasta sequences from the same run), the sequences did…
-
I am trying to run this but it has been running for over a week on the iqtree step. Is there a way to speed that up? It is running on a 64 core machine, but I see that iqtree decided that 2 cores was …
-
Using the attached alignment and this code within a jupyter notebook
```python
from cogent3 import get_app, load_aligned_seqs
aln = load_aligned_seqs("ENSG00000000971.fa", moltype="dna")
phylo…
-
Hello,
I am trying to run contrast-fel on HPC using this command:
hyphy fel --alignment nt.fasta --tree tree.nexus --branches --output nt.json
The tree is a tree rescaled in time with ancest…
-
I understand mosh does _something_ with respect to ANSI escape sequences, but I don't quite understand it. Using ssh, running the 'tree' command looks like this:
```
$ tree
.
├── [ 0] one
├─…
-
Hi! I'm writing with a question about input matrix size limits. I have a large alignment file-- 158 individuals, 49M sites, and I'm getting a segmentation fault error. Do you have any recommendations …
-
Hello,
I am trying to run MEME on HPC on several fasta file but I'm getting this error:
Error:Illegal right hand side in call to Topology id = ...; it must be a string, a Newick tree spec or a t…
-
From branch 35 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1502
JN.1.4+T18453C+G28209C,del21653_21655(Orf8:E106Q, S:S31-)+G22599C(S:R346T)
Brazil just uploads a lot of seq…