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![image](https://cloud.githubusercontent.com/assets/27538/22975790/db0867ce-f355-11e6-838e-2f13c84a1857.png)
The example above showcases what I'm trying to do: the first line has two insertions ("v…
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It might be a bit far-fetched, but per this [reddit thread](https://www.reddit.com/r/emacs/comments/14s803p/editmode_for_pointbypoint_text_proofreading_like/) I still try to post my feature idea here.…
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CollateX will crash with the following error
```
Unexpected error
null
```
when run with the following JSON input file:
``` json
{
"witnesses" : [
{
"id" : "base",
…
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A missing feature in the alignment package is that of semiglobal alignments, useful for aligning a short query sequence against a large target database (e.g. a genome).
See [this wikipedia paragraph]…
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currently it's using cogent aligners, which are likely a lot slower. this change will improve the run time and remove the cogent dependency. depends on skbio's [#117](https://github.com/biocore/scikit…
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The pdb-to-uniprot alignments we get for some entries don't seem right, e.g.
1ozv.A, the n-terminus looks like this:
```
1 …
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Hi, I'm having a problem when trying to simulate a file with lines starting with # (which are comments according to the Paje specification). Here's what I got:
$ java br.ufrgs.inf.tlbellini.PajeGramm…
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Hi,
This is more of a question than an issue.
I was playing around with `mmseqs alignall` intending to see how it works. I think maybe it is in development.
I took a cluster I had and run `al…
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The function in clustering is originally taken from and builds on lingpy's infomap-clustering (you might want to mention this in the function description), and it has some code that you never use:
…