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![alignment](https://user-images.githubusercontent.com/13358837/46524084-490f1e80-c8ba-11e8-9a69-a669aa83b1c1.png)
In my training with my own data the loss converges rapidly, though as well as the al…
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I've been playing around with GARD and ran it on 10 and 20 randomly sampled Pango sequence founders.
When I tried it out on 27 sequences, however, I got an error:
```
hyphy gard --alignment sa…
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I'd like to remove parts of alignments that have low identity. The idea would be to take a longer alignment and break it into multiple alignments, removing regions where the identity drops below some …
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For some applications, such as protein-RNA complexes, I'd like to pair sequences by a custom method- and input already paired seqs (2 alignments where sequence X in ali 1 is paired with sequence X in …
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Top-scoring alignments with scores well over the relevant threshold seem to be discarded when they also contain insertions. For instance, the following V alignment will not be included in the n_V_alig…
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more explanatory errors (espec for uploading 2 alignments with different sequences)
TS404 updated
8 years ago
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Hi,
I successfully run orthofinder using the protein sequences, but I get an error when I run it again using the nucleotide sequences from the same species.
I have DNA sequences for 71 species. Th…
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Hi,
I'm trying to run cactus-align (v2.8.4) skipping the Splitting By Chromosome step with the following comand:
cactus-align ./jobstore asmhifi_217.txt cactus1.paf cactus1.hal --pangenome --out…
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Hello,
I have been playing around with the alignments in the output folder and I noticed that many of the alignments have duplicate IDs, for instance in RF00008, URS000080DE02_31504/1-69 appears at…
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**Describe the issue**
RepeatMaskerLib.embl is not built while configuring RepeatMasker-4.1.2-p1 and is requestrd by DateRepeats
```
rpm_maker:RepeatMasker/RepeatMasker-4.1.2-p1 > DateRepeats
I…