Kenji Fukushima
Kenji Fukushima
Hi, Thank you for the development and maintenance of this useful package. With the latest GitHub version of pypdb, I tried to run MMseqs2 searches of many sequences using `Query`...
**Are you using the latest release?** yes, 1.8.8. **Describe the bug** At the moment, `funannotate mask` does not seem to support RepeatModeler 2.x. This is because the `RepeatModeler -e` option...
Thank you for the development and maintenance of IQ-TREE. I am reporting unexpected NaNs in the .state file I got in only one out of 100 alignments I am analyzing....
With python 3.9, I got the following error with `python setup.py install` when installing the latest SubPhaser. ``` > python setup.py install error in subphaser setup command: 'python_requires' must be...
I needed a couple of tricks for using WGDdetector installed from conda. Here I am sharing my experience in case it is useful to someone else. First I installed WGDdetector...
- `--mode intersection`: default. Visualizing combinatorial substitutions of branches specified by `--branch_id`. Generating 1 pse. - `--mode total`: Color intensity according to the number of all amino acid substitutions in...
``` CSUBST command: csubst analyze --max_arity 3 --threads 4 --alignment_file alignment.fa --rooted_tree_file tree.nwk --iqtree_redo no --fg_exclude_wg no --fg_stem_only no --fg_format 2 --foreground foreground.tsv --exhaustive_until 1 --fg_clade_permutation 10 CSUBST working directory:...
In the current implementation, --fg_clade_permutation should be combined with --exhaustive_until to randomize branch combinations properly. If this requirement is not fulfilled, CSUBST reports it as below. CSUBST should re-calculate missing...
This would significantly save RAMs in extremely large trees.
The visualized sites should be the same as shown in the protein structure, and may be organized as: convergent sites, blank, divergent sites.