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Hello,
I was wondering if maybe there is a way to use `pxclsq` to remove codons instead of single sites; something similar to what this [script](https://bitbucket.org/yangya/caryophyllales_mbe_2015…
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Drag drop the file to panel. After select the genetic code, the file seems disappear.
AlignmentListInputEditor needs to improve:
```java
table.setOnDragDropped((DragEvent event) -> {
…
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Cannot delete partition after the codon alignment is loaded. It seems`delItem()` is not working for `CodonAlignment`.
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Dear Osamu, @ogotoh
I followed your instruction from [issue 77](https://github.com/ogotoh/spaln/issues/77) to successfully map and align protein sequences to a genome. However, the "match format"…
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Hi,
I'm running hivmmer using the conda environment as detailed in the manual, but it fails on report generation:
_hivmmer -o /home/jpflorido/GBPA/tmp/VIH/himmer/ -t 12 DRR030218_1.fastq DRR030218…
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When I concatenate the alignments into the PCGs12RNA dataset, check the “Split codon” checkbox, and check both the “first codon site” and “second codon site” checkboxes ,this error appeared. PhyloSuit…
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There are a lot of comments but they give much useful information. For example:
```
///
/// Holds a single residue codon, and a list of its features
///
struct Residue {
Residue(std::stri…
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陈老师，您好，我在跑geta的第二步2.homolog_prediction时，出现以下报错：
failed to execute: /public/home/geta/bin/homolog_prediction --tmp_dir /public/home/project/1_cooperate/FX-geta/FX.tmp/2.homolog_prediction --cpu 30 --i…
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It appears that when diamond blastx encounters a codon that contains a nucleotide IUPAC ambiguity code , "RYWSMKHBVDN", the resulting amino acid is "X"; however, in some cases, codons that contain a n…
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For proteins mapping to multiple contigs/chromosomes, how might one deduce the equivalent of mapping quality with miniprot? My guess is one could have a go at AS and as scores (although I am seeing `m…