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Request that add some @amandamok's simulated ribosome profiling data into RiboViz as another vignette. This should provide ideal testing that reads are correctly aligned and of codon-level and gene-le…
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We have not been able to run codon models in iqtree despite using what we think is the correct command line:
`iqtree -s example.nex -st CODON -m KOSI07`
The program reports for a small example …
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---
Author Name: **Albert Vilella** (Albert Vilella)
Original Redmine Issue: 2078, https://redmine.open-bio.org/issues/2078
Original Date: 2006-08-17
Original Assignee: Bioperl Guts
---
I think it …
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I am trying to obtain the global kappa value, I have found that I can do this in the command line using the interactive tool by selecting the following:
```
(5) Basic Analyses
(1) Analyse codon d…
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Hi, thanks for writing this brilliant intactness pipeline.
I've had some trouble getting it to work and I think it's due to python incompatibility.
```
Invalid command line
Unknown option in
…
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```
hp_pairwise_align --amplicons_fa haphpipe_assemble_02/final.fna --ref_fa ../HIV_B.K03455.HXB2.fasta --ref_gtf ../HIV_B.K03455.HXB2.gtf --outdir haphpipe_assemble_02
[--- pairwise_align ---] U…
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Hi!
I am using Hmmer3 with bivalve genomes looking for 70-80 aa genes. BUSCO scores for the genomes are in the upper 90s (96-98% complete for BUSCO Metazoa) and most assemblies are chromosome-scale…
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@cebos found that the output from Concatenator includes both the full genes and the genes subsetted by codon position. Not sure if this is the desired behaviour? PartitionFinder only wants the codon p…
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**Describe the bug**
Currently `mehari db build` will skip the transcript `NM_001291324.3` in the GRCh37 transcript alignments (as the alignment has no stop codon in the CDS). However, it mention…
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## Expected Behavior
easy-search should finish execution without errors
## Current Behavior
Error during pre-filter step
> Index table k-mer threshold: 0 at k-mer size 15
> Index table: …