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Available analysis command line options
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Use --option VALUE syntax to invoke
If a [reqired] option is not provided on the command line, the analysis will prom…
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Hi,
I am using PRANK v.170427.
I am having trouble with codon alignment. When I execute the line of code
`prank -d=OG0017868.ffn -o=prank_test_out -F -codon`
I get the following errors
…
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For proteins mapping to multiple contigs/chromosomes, how might one deduce the equivalent of mapping quality with miniprot? My guess is one could have a go at AS and as scores (although I am seeing `m…
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hi there,
I've been reading in some multiple sequence alignments, as DNAStringSet objects. They're nucleotide alignments that encode proteins. I've been playing with using 'translate', but it looks…
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Hello! Hope this message finds you well.
I've just used ete3 to run codeml on a series of alignments. I ran models bsA and bsA1 to test for positive selection, but I'm havinf issues with interpreti…
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
```python
>>> import sys; print(sys.version)
3.5.2 (default, Nov 23 2017, 16:37:01)…
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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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Hi,
I am trying to use the codon-msa pipeline to make my alignment more codon aware. I am encountering this issue when I run the pre-msa.bf it starts the analysis but then throws errors like below:…
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Author Name: **Prachi Shah** (Prachi Shah)
Original Redmine Issue: 2069, https://redmine.open-bio.org/issues/2069
Original Date: 2006-08-10
Original Assignee: Bioperl Guts
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I am trying to al…
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Hi @imk1,
Although I know that the main purpose of HLPER is not to transfer protein-coding genes, I wonder if Halpes has been tested for this task.
Let me explain my problem: I have two non-model …