pyGenomeViz
clinker
pyGenomeViz | clinker | |
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3 | 2 | |
231 | 502 | |
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8.3 | 3.2 | |
7 months ago | 10 months ago | |
Python | Python | |
MIT License | MIT License |
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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
clinker
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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?
itermplot - An awesome iTerm2 backend for Matplotlib, so you can plot directly in your terminal.
ncbi-genome-download - Scripts to download genomes from the NCBI FTP servers
mummer - Mummer alignment tool
pyCirclize - Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
quast - Genome assembly evaluation tool
gggenomes - A grammar of graphics for comparative genomics
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)
dash - Data Apps & Dashboards for Python. No JavaScript Required.
FastANI - Fast Whole-Genome Similarity (ANI) Estimation
scanpy - Single-cell analysis in Python. Scales to >1M cells.