BRAKER
BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes (by Gaius-Augustus)
Prodigal
Prodigal Gene Prediction Software (by hyattpd)
| BRAKER | Prodigal | |
|---|---|---|
| 2 | 4 | |
| 321 | 406 | |
| 1.9% | - | |
| 8.7 | 0.0 | |
| 9 days ago | 3 months ago | |
| Perl | C | |
| GNU General Public License v3.0 or later | GNU General Public License v3.0 only |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
BRAKER
Posts with mentions or reviews of BRAKER.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-06-05.
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Annotation of fungal genomes
Braker looks reasonable, though I only really have been doing bacterial genome annotation.
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ORF prediction for non-model organism with DNA sequence only
BRAEKR2 (include GeneMark + AUGUSTUS, can take RNA-seq and OrthoDB in consideration)
Prodigal
Posts with mentions or reviews of Prodigal.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-06-19.
-
DNA to amino acid sequence?
use prodigal https://github.com/hyattpd/prodigal
- Trying to Install Prodigal from GitHub
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ORF prediction for non-model organism with DNA sequence only
I'd use prodigial and not their ugly closed source software...
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How do I convert a scaffold into genes?
Prodigal is a commonly used gene-caller for prokaryotic genomes. In fact, I believe it is used by Prokka, as mentioned by another commenter.
What are some alternatives?
When comparing BRAKER and Prodigal you can also consider the following projects:
prokka - :zap: :aquarius: Rapid prokaryotic genome annotation
funannotate - Eukaryotic Genome Annotation Pipeline
pyrodigal - Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
DNA-to-Protein-sequence - Translate a string containing a nucleotide sequence(DNA) into a string containing the corresponding sequence of amino acids.
DNA-to-Amino-Acid-Converter - This program breaks apart a DNA string and dispalys each amino acid associated with each codon