phantasm
PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes (by dr-joe-wirth)
pyGenomeViz
A genome visualization python package for comparative genomics (by moshi4)
| phantasm | pyGenomeViz | |
|---|---|---|
| 2 | 3 | |
| 24 | 312 | |
| - | 2.9% | |
| 8.6 | 8.7 | |
| over 1 year ago | 2 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.
phantasm
Posts with mentions or reviews of phantasm.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-04-02.
- Is there any way to easily create a docker image that has both python and R?
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PHANTASM: new software for microbial taxonomy
The easiest way to try it out PHANTASM is to use the Docker image. The source code is also available on github.
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
What are some alternatives?
When comparing phantasm and pyGenomeViz you can also consider the following projects:
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
itermplot - An awesome iTerm2 backend for Matplotlib, so you can plot directly in your terminal.
drep - Rapid comparison and dereplication of genomes
DnaFeaturesViewer - :eye: Python library to plot DNA sequence features (e.g. from Genbank files)
pyani - Application and Python module for average nucleotide identity analyses of microbes.
pyCirclize - Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)