pyGenomeViz
A genome visualization python package for comparative genomics (by moshi4)
clinker
Gene cluster comparison figure generator (by gamcil)
| pyGenomeViz | clinker | |
|---|---|---|
| 3 | 2 | |
| 319 | 566 | |
| 3.4% | 2.3% | |
| 8.1 | 5.4 | |
| 9 days ago | 5 months ago | |
| Python | Python | |
| MIT License | MIT License |
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.
pyGenomeViz
Posts with mentions or reviews of pyGenomeViz.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-10-01.
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How to perform Genome Alignment ?
Do you want to perform a whole genome alignment between species? I often use the following software for genome alignment in prokaryotes and viruses. - MUMmer (pairwise genome Aligner) - progressiveMauve (Multiple Genome Aligner) Due to the high mutation frequency of viral genomes, it is sometimes difficult to compare them at the nucleotide sequence level. Therefore, it may be better to make comparisons at the protein level with MUMmer for viral genomes. I have recently developed the software pyGenomeViz, which automates the process of performing and visualizing whole genome alignments, so check it out if it seems to fit your needs.
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Software to make in-scale illustrations of genomic locations
If you can build a Python environment and do a little coding, DnaFeaturesViewer or pyGenomeViz would be good choices. You can generate the following figure from a Genbank file with about 10 lines of code. Of course, you can specify the range of coordinates to be plotted.
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pyGenomeViz: A genome visualization python package for comparative genomics
GitHub repo: https://github.com/moshi4/pyGenomeViz
clinker
Posts with mentions or reviews of clinker.
We have used some of these posts to build our list of alternatives
and similar projects.
-
Need help with protein gene-neighborhood methods.
Being a silent reader all this while, this is my first question here and a very basic indeed. I want to generate some gene neighborhood clusters for a set of protein fasta files I have from UniProtKB. I plan to use: 1. http://www.webflags.se/ and 2. https://github.com/gamcil/clinker
- Stuck Running Bioinformatics Tool Through Command
What are some alternatives?
When comparing pyGenomeViz and clinker you can also consider the following projects:
itermplot - An awesome iTerm2 backend for Matplotlib, so you can plot directly in your terminal.
MultiQC - Aggregate results from bioinformatics analyses across many samples into a single report.
DnaFeaturesViewer - :eye: Python library to plot DNA sequence features (e.g. from Genbank files)
quast - Genome assembly evaluation tool
pyCirclize - Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)