itermplot
pyGenomeViz
| itermplot | pyGenomeViz | |
|---|---|---|
| 2 | 3 | |
| 1,480 | 227 | |
| - | - | |
| 0.0 | 8.3 | |
| 11 months ago | 6 months ago | |
| Python | Python | |
| - | MIT License |
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itermplot
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UnicodePlots
If you happen to use `iTerm2`, then https://github.com/daleroberts/itermplot works very well. I've used it before and can recommend it pretty highly.
- iTerm2 back end for Matplotlib – plot directly in your terminal
pyGenomeViz
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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?
termplotlib - :chart_with_upwards_trend: Plotting on the command line
mummer - Mummer alignment tool
LDV-plotter - This is a mathematics functions plotter. With this tool you can create beautiful plots and surprise your friends.
pyCirclize - Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
tv - Quickly view (satellite) imagery directly in your terminal using Unicode 9.0 characters and true color.
gggenomes - A grammar of graphics for comparative genomics
yellowbrick - Visual analysis and diagnostic tools to facilitate machine learning model selection.
DnaFeaturesViewer - :eye: Python library to plot DNA sequence features (e.g. from Genbank files)
seaborn-image - High-level API for attractive and descriptive image visualization in Python
FastANI - Fast Whole-Genome Similarity (ANI) Estimation
bitrate-variation-plotter - Plots a graph showing the bitrate every second or the bitrate of every GOP, for an audio or video file.
AGAT - Another Gtf/Gff Analysis Toolkit