Comments (4)
Hi @Bunholi,
Unfortunately, the corrections did no solve the problem.
I think that it is a software issue.
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Hi,
I've managed to re-run your analysis for Asteracea and I'm looking over the clusters. So that I can repeat your process, how are you determining that there is a mix of ITS and trnL in the first cluster?
The top thing I've noticed is ...
#specify the sequence IDs per cluster
sids <- reduced@clstrs[[i]]@sids
Should be:
#specify the sequence IDs per cluster
sids <- selected@clstrs[[i]]@sids
Where does the "reduced" phylota object originate? Mixing sids across different phylota objects could be causing the mixing of sequences in a cluster.
from phylotar.
Hi @bpjburger did you solve the problem following @DomBennett correction?
I am planning to do the same around here
from phylotar.
For info, we're looking for a new maintainer / a new maintainer team for this package, see #57 and feel free to volunteer, we'd be happy to help.
from phylotar.
Related Issues (20)
- problem with the restez/phylota integration
- Possibility to supply NCBI API key when running pipeline to access NCBI data faster? HOT 1
- Use phylotaR for retrieving orthologous protein sequences HOT 1
- No periods or tildes in file paths HOT 3
- Can not install the package in windows HOT 2
- Clusters with different parent number but the same MAD, seed, length, n_taxa, n_seqs
- Description - not enough information
- New Maintainer Wanted HOT 5
- Next release HOT 6
- CRAN archive of package outsider
- Fix pkgdown configuration for reference HOT 3
- No need for restez_connect() HOT 1
- Remove treeman as a dependency? HOT 2
- Could get something new from https://github.com/pachterlab/gget
- test failure HOT 1
- Generating taxonomic dictionary error HOT 1
- Fetch and error seem to be stuck HOT 2
- drop taxa functionality HOT 1
- Identical clusters making it into alignments HOT 1
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