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Need to add functionality to lift co-ordinates in one sequence over to the other sequence in pairwise alignments. This should take into account gaps, and might return more than one genomic interval if…
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Hi Felix,
I have a couple of questions regarding Bismark. I'm sorry if they are stupid questions; I am fairly new to WGBS data and Bismark analysis (or to bioinformatics in general).
We are rese…
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Hello!
When it comes to structural variant calling, one characteristic of the presence thereof is a noisier sequence than usual. With these noisy sequences, the secondary alignment can then provide…
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```
What steps will reproduce the problem?
1. prank -d=EOG78Q418.fa -o=EOG78Q418
2. Same problem whether using prank compiled from source or pre-made binary
3. prank works well for the vast majority o…
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#### System info
```python
import sys; print(sys.version)
import platform; print(platform.python_implementation()); print(platform.platform())
import Bio; print(Bio.__version__)
```
```
3.8.19…
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I want to only use the genetic distance from inputted sequence alignments to get the cut-off values, is that possible?
BTW, if construct trees, can I use other softwares, like fasttree, phyml, raxml?
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Hi,
I'm really interested in using graphmap for doing some Nanopore alignments with predicted sequences but I can not seem to get an alignment. I tried to get an alignment with a simple sequence ju…
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Hello everyone,
I'm running orthofinder and I faced with a problem at step making gene tree (MSA). It's warning that list index out of range. and the number of ortholog is low percentage (40%).
Doe…
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Hi,
I am using the recomputed_alignments_mmseqs.py to search for MSA for my input.fasta which has 9 sequences inside.
but the mmseq2 is taking too long to run it, it is already over 4 hours, but st…
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Hello,
Our lab has been using hifiasm for a number of genome assembly projects. We are using Nanopore reads (kit 14 chemistry, R10.4.1 flow cells) that have been error-corrected with PECAT or HERRO…