pyGenomeViz
A genome visualization python package for comparative genomics (by moshi4)
mummer
Mummer alignment tool (by mummer4)
| pyGenomeViz | mummer | |
|---|---|---|
| 3 | 2 | |
| 229 | 421 | |
| - | 2.1% | |
| 8.3 | 0.0 | |
| 7 months ago | about 2 months ago | |
| Python | C++ | |
| MIT License | Artistic License 2.0 |
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
mummer
Posts with mentions or reviews of mummer.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-10-01.
-
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.
-
MSA of whole bacterial genomes, how do I do it?
I often used the following tools for prokaryotic genome alignment. Genome alignment between two species => MUMmer (pairwise genome aligner)
What are some alternatives?
When comparing pyGenomeViz and mummer you can also consider the following projects:
itermplot - An awesome iTerm2 backend for Matplotlib, so you can plot directly in your terminal.
pyCirclize - Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
gggenomes - A grammar of graphics for comparative genomics
DnaFeaturesViewer - :eye: Python library to plot DNA sequence features (e.g. from Genbank files)
FastANI - Fast Whole-Genome Similarity (ANI) Estimation
AGAT - Another Gtf/Gff Analysis Toolkit
tinycov - Command line tool to plot genomic coverage from a BAM file
clinker - Gene cluster comparison figure generator
ncbi-genome-download - Scripts to download genomes from the NCBI FTP servers