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We were aligning a paired-end sequenced ancient DNA sample, where the reads were merged when they appear to overlap in order to reduce the sequencing error rate and improve alignment accuracy in the f…
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What would be the command line parameters for `parasail_aligner` for doing local pairwise alignment (without gaps within the sequences) of two DNA sequences
For example, `1.fa` is like this
```
…
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-searching for reference exome (CDS) as a reference for our exome sequence data due to several reasons:
1- when we aligned to one chromosome like chr 20, the alignment rate was v.v low 2.8%
2- whe…
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Hi Jim
PrimerTree is a very handy tool! Recently when I ran the package, I got this error. I attached the output here. Do you know if it's because there's too many blast hits?
> Primer = search_prime…
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Hi,
I have an alignment file generated from snippy. Now I am using IQ-Tree with 480 sequences for constructing phylogenetic tree. I ran IQ-tree with the following command. However, it is taking so lo…
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At least for `sangerseqR_1.34.0`, one can provide a reference for `SangerContig()`, but it must be an amino acid sequence (`refAminoAcidSeq=`), so non-coding genes (e.g., 16S rRNA) are not supported. …
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For #2046 I am trying to remove the use of the ``Gapped`` class, and adding explicit defaulting to ``"-"`` as a gap character where necessary.
The ``to_alignment`` method tests in ``test_PhyloXML.p…
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Hi,
Thanks for the hard work on this tool.
I managed to hit a core dump when `amrfinder` runs `blastn` when running in multi-threaded mode.
Here are the logs:
```
(amrtest) root@8a9053f3c7c…
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Hi,
After running EG with v4.2.4 for a while without major problems, we upgraded to 4.4.0 recently and have a couple issues.
It seems one issue is with TEstrainer where run time explodes into we…
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The manual says:
"protein2genome
This model allows alignment of a protein sequence to genomic DNA. This is similar to the protein2dna model, with the addition of modelling of introns and intron phas…