philipwoods

## Short description of the problem Running `anvi-summarize` on a pan database using the `--quick-summary` option gives a gene cluster summary file where the output columns don't line up with...

The NetLogo Web info tab doesn't accurately render newlines in some situations. When there is only a single newline between lines, the Web info tab doesn't separate the lines, which...

[BUG] `anvi-run-hmms` does not accurately detect 5S rRNA

8

## Short description of the problem Even in single-contig circularized genomes, `anvi-run-hmms` does not reliably detect the 5S rRNA gene. ## anvi'o version ``` Anvi'o .......................................: marie (v8) Python .......................................:...

[BUG] Pandas dataframe has no attribute 'append'

4

## Short description of the problem `anvi-analyze-synteny` fails because Pandas has deprecated `DataFrame.append()` as of version 1.4.0 in favor of `pandas.concat()`. ## anvi'o version ``` Anvi'o .......................................: marie (v8) Python...

[BUG] Pandas error in `anvi-get-codon-frequencies`

6

## Short description of the problem When running `anvi-get-codon-frequencies`, there is a TypeError in how pandas is used in `_make_gene_codon_frequency_table`. ## anvi'o version ``` Anvi'o .......................................: marie (v8) Python .......................................:...