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Hi,
When working with metabarcoding data where you're not interested in any specific taxonomic group but want to quantify general diversity, you almost always have a mix of different genetic codes …
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I am trying to use maf_parse to split a maf generated from a [hal](https://github.com/ComparativeGenomicsToolkit/hal), which has some blocks where the same source sequence is included multiple times. …
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The gene alignment step can take a long time to complete. Is it possible to add functionality to output the unaligned gene sequences to later align batches of them across a computing cluster? The pira…
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Hello,
I run bamquery
```python
!python xxx/Software/bamquery/BamQuery/BamQuery.py xxx/Software/bamquery/BamQuery try_1 v38_104 --mode normal --t 8 --plots
```
And my output is as follows,
`…
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Spurred on by #12 -
This package is old as dirt (it still has a `REQUIRE` file from pre-Pkg days), and only contains one tool - BLAST. If I recall correctly, this package was initially intended as …
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Hi David,
I'm using Orthofinder to analyze 19 species, and the mission is stuck. The supercomputer I rented has been running for a dozen days and still hasn't run 19 species. The commands I use are a…
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The "Inferring remaining multiple sequence alignments and gene trees" has been ended by our SLURM scheduler due to time limit. Only 6 jobs out of 35000 were still running. Is it possible to run them m…
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Hi!
I have a question regarding handling of sequences with different length.
I usually align sequences with a fixed identity cutoff of 97% and, depending on the sample, different read length. `v…
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Hello!
I'd like to kindly ask if is it possible to add support to inputs baring asterisk "*" character.
This one I tested was made with [sam2fasta.py](https://sourceforge.net/p/sam2fasta/tickets/):
…
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Maybe the MAFFT output doesn't give the proper format for your tool to run, but I am not getting correct looking results. Can you look at what MAFFT outputs here:
http://mafft.cbrc.jp/alignment/server…