biopython

There are 17 repositories under biopython topic.

biopython / biopython
Official git repository for Biopython (originally converted from CVS)
python bioinformatics genomics biopython protein protein-structure sequence-alignment phylogenetics dna
Language:Python 4165
dash-cytoscape
plotly / dash-cytoscape
Interactive network visualization in Python and Dash, powered by Cytoscape.js
plotly-dash plotly dash cytoscape cytoscapejs network-visualization network-graph graph-theory bioinformatics computational-biology data-science biopython
Language:Python 571
ponnhide / pyCircos
python Circos
biopython circos circos-plot matplotlib phylogenetic-trees python visualization
Language:Python 306
modernatx / seqlike
Unified biological sequence manipulation in Python
sequence biological-sequences biopython machine-learning
Language:Python 201
pydna
BjornFJohansson / pydna
Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
bioinformatics biopython python anaconda dna gel jupyter-notebooks biology pydna jupyter-notebook gel-simulation jupyter gibson-assembly cloning-strategies gel-electrophoresis assembly-strategies simulation genbank fasta
Language:Jupyter Notebook 152
wheretrue / biobear
Work with bioinformatic files using Arrow, Polars, and/or DuckDB
bioinformatics biology rust-bio samtools arrow python biopython duckdb polars pyarrow
Language:Rust 120
cogent3 / cogent3
Comparative Genomics Toolkit 3
bioinformatics pycogent statistics data-science biology genomics evolution biopython markov-chain molecular-evolution non-stationary phylogenetic-trees phylogenetics python parallel signal-processing maximum-likelihood biological-sequence-analysis sequence-alignment
Language:Python 93
biopython-coronavirus
chris-rands / biopython-coronavirus
Biopython Jupyter Notebook tutorial to characterize a small genome
bioinformatics biopython coronavirus covid-19 genomics jupyter-notebook python
Language:Jupyter Notebook 88
Zsailer / phylopandas
Pandas DataFrames for phylogenetics
phylogenetics python pandas biopython
Language:Python 69
pyladies-brazil / grupo-estudo-bioinformatica
Repositório do grupo de estudo de Bioinformática da rede de comunidades das PyLadies Brasil.
bioinformatics bioinformatics-pipeline bioinformatics-analysis biopython rosalind estudo
Language:Jupyter Notebook 40
yachielab / QUEEN
QUEEN: a framework to generate quinable and efficiently editable nucleotide sequence resources
bioinformatics biopython plasmids jupyter-notebooks
Language:Python 34
RKMlab / perf
PERF is an Exhaustive Repeat Finder
biopython fasta genome genomics microsatellites repeats sequence simple ssr tandem
Language:HTML 33
RK900 / Flu-Prediction
Predicting Future Influenza Virus Sequences with Machine Learning
biopython dna flu flu-prediction machine-learning python scikit-learn
Language:Python 30
phyTreeViz
moshi4 / phyTreeViz
Simple phylogenetic tree visualization python package for phylogenetic analysis
phylogenetic-trees bioinformatics biopython matplotlib python visualization
Language:Python 25
widdowquinn / 2018-03-06-ibioic
Teaching materials for 6-7th March 2018 delivery of introductory bioinformatics training course for IBioIC.
teaching teaching-materials bioinformatics blast uniprot python biopython jupyter-notebook
Language:HTML 20
GBKviz
moshi4 / GBKviz
Easy-to-use web application for visualization and comparison of genomes in Genbank file
bioinformatics genomics genomics-visualization genbank comparative-genomics webapp streamlit biopython python microbial-genomics visualization
Language:Python 19
biocpp / biocpp-core
BioC++ core library (alphabet, meta, ranges)
biocpp biopython cpp cpp20 dna protein sequence-analysis cpp-library header-only metaprogramming ranges
Language:C++ 18
Protein-feature-extraction
jithin8mathew / Protein-feature-extraction
Python code to extract features from Protein sequences for Machine Learning/Deep Learning
protein-feature-extraction machine-learning protein-sequences biopython deep-learning linux extract-features fasta feature-extraction windows bioinformatics-pipeline bioinformatics-data bioinformatics-analysis bioinformatics
Language:Python 17
laelbarlow / amoebae
Workflow for identifying and classifying homologous gene/protein sequences
bioinformatics hmmer3 biopython python3 blast genome-annotation similarity-search coulson-plot transcriptome-annotation snakemake-workflow comparative-genomics homology molecular-evolution gene-families protein-families orthology
Language:Python 17
Edinburgh-Genome-Foundry / SnapGeneReader
👓 Python library to parse Snapgene *.dna files to dict or biopython seqrecord.
synthetic-biology sequence-design converter genbank biopython snapgene
Language:Python 16
biosustain / goodbye-genbank
A Python package for Biopython that gives feature annotations from GenBank records a new and better life
biopython genomics genbank sequence-ontology gff3
Language:Python 14
rodogi / biographs
Python class to easily deal with protein networks.
amino-acid-network protein-contact-network protein-structure biopython
Language:Python 14
althonos / orthoani
A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
average-nucleotide-identity orthoani python python-module biopython bioinformatics
Language:Python 13
nalomran / pubmed2doc
Write PubMed search results with two display options (citation or listview) to PDF or Word
bioinformatics pubmed pubmed-parser python3 biopython fpdf docx
Language:Python 13
vinisalazar / BioProv
A provenance library for bioinformatics workflows 🧬 🔀 📝
w3c-prov biopython biological-data provenance python prov
Language:Python 13
althonos / moclo
Modular cloning simulation with the MoClo framework in Python
system-biology modular-cloning plasmids biopython bioinformatics moclo
Language:Python 12
bott0n / Needleman-Wunsch-Algorithm
Needleman-Wunsch Algorithm for global alignment and local alignment
biopython neeldman-wunsch algorithm local-alignment global-alignment dna protein sequences
Language:Python 11
dewshr / NCBI-GenBank-file-parser
This program can be used to parse the NCBI GenBank file to create a tabulated csv file.
ncbi-genbank parser biopython extract-data extract-information reference-data metadata python file-parser
Language:Python 10
kirai / bio_hacking
Biotech with biopython
biotechnology biopython
Language:Python 9
biocpp / biocpp-io
BioC++ Input/Output library
biocpp fasta fastq fastq-format bcf bcftools biopython cplusplus-20 fasta-format header-only modern-cpp seqan sequence-analysis vcf vcf-format csv input-output tsv c-plus-plus
Language:C++ 8
primerdriver
kvdomingo / primerdriver
PrimerDriver - Automated design of mutagenic PCR primers
mutagenic-pcr-primers polymerase-chain-reaction primer-design site-directed-mutagenesis command-line web-application python react cli biopython
Language:Python 8
dillondaudert / proteindatasets
Creating and manipulating various protein sequence-structure datasets using Python, Julia, and other tools.
bioinformatics biopython blast dataset dssp fasta julia jupyter jupyter-notebook pandas protein psiblast python3 secondary structure tensorflow uniref50
Language:Jupyter Notebook 6
raghurama123 / PyLifeS
A graduate-level elective course: Python Programming for Life Science Students
biology biology-education python bioinformatics biopython computational-biology
Language:Jupyter Notebook 6
weisscharlesj / BiopythonRamachandran
biochemistry bioinformatics biopython jupyter jupyter-notebook pdb python ramachandran-plot visualization
Language:Jupyter Notebook 6
SARS-CoV-2-ORF3d
chasewnelson / SARS-CoV-2-ORF3d
Supplementary scripts for Nelson et al. (2020) paper on ORF3d
covid-19 sars-cov-2 overlapping-genes orf3d olgenie perl python r snpgenie within-host between-host biopython
Language:R 5
MountainMan12 / SARS-Cov2-phylo
Analysis of the viral genomes of SARS-CoV2 using MAFFT and igtree
multiple-sequence-alignment phylogenetic-trees ncbi-database biopython
Language:Python 5