Alternatives and similar repositories for pathogenie

Users that are interested in pathogenie are comparing it to the libraries listed below

• dbikard / genomenotebook
  A genome browser in your Jupyter notebook
  ☆31Updated 2 months ago
• salzberg-lab / Balrog
  Bacterial Annotation by Learned Representation of Genes
  ☆57Updated 4 years ago
• Edinburgh-Genome-Foundry / Geneblocks
  Find common blocks and differences between DNA sequences
  ☆42Updated 3 months ago
• mckennalab / Circuitseq
  Nanopore Plasmid Sequencing
  ☆33Updated last year
• KatyBrown / CIAlign
  ☆131Updated 10 months ago
• BolognaBiocomp / deepsig
  DeepSig - Predictor of signal peptides in proteins based on deep learning
  ☆26Updated 2 years ago
• glarue / jgi-query
  A simple command-line tool to download data from Joint Genome Institute databases
  ☆52Updated 2 years ago
• ponnhide / plasmidviewer
  Python library to visualize circular plasmid maps
  ☆26Updated 3 years ago
• althonos / pyfamsa
  Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.
  ☆32Updated last month
• LaboratorioBioinformatica / MARVEL
  MARVEL: Metagenomic Analyses and Retrieval of Viral ELements
  ☆53Updated last year
• mmcguffi / pLannotate
  Webserver and command line tool for annotating engineered plasmids
  ☆123Updated this week
• jrjhealey / bioinfo-tools
  Just a collection of (often poor) scripts to do various bits of bioinformatics stuff I find myself needing to do.
  ☆59Updated 4 years ago
• morgannprice / PaperBLAST
  PaperBLAST: find papers about a protein or its homologs
  ☆40Updated last week
• smirarab / sepp
  Ensemble of HMM methods (SEPP, TIPP, UPP)
  ☆91Updated 10 months ago
• steineggerlab / conterminator
  Detection of incorrectly labeled sequences across kingdoms
  ☆85Updated 2 years ago
• Adrian-Cantu / PhANNs
  ☆20Updated 2 years ago
• jambler24 / GenGraph
  A repository for the GenGraph toolkit for the creation and manipulation of graph genomes
  ☆51Updated 3 years ago
• EnzoAndree / HmmPy
  A Pure-Python parser of HMMER3 output
  ☆17Updated 9 months ago
• bioforensics / pytaxonkit
  Python bindings for the TaxonKit library
  ☆41Updated 3 weeks ago
• deprekate / PHANOTATE
  PHANOTATE: a gene caller for phages.
  ☆78Updated 7 months ago
• bhattlab / SmORFinder
  A command line tool to identify and annotate small proteins in microbial sequencing datasets.
  ☆24Updated 2 years ago
• BigDataBiology / macrel
  Predict AMPs in (meta)genomes and peptides
  ☆81Updated last month
• PedroMTQ / mantis
  A package to annotate protein sequences
  ☆59Updated 4 months ago
• rnajena / vidhop
  VIDHOP is a virus host predicting tool. Its able to predict influenza A virus, rabies lyssavirus and rotavirus A.
  ☆22Updated 2 years ago
• RyanCook94 / inphared
  Providing up-to-date phage genome databases, metrics and useful input files for a number of bioinformatic pipelines.
  ☆67Updated 3 months ago
• niemasd / TreeCluster
  Efficient phylogenetic clustering of viral sequences
  ☆87Updated last year
• sanger-pathogens / Fastaq
  Python3 scripts to manipulate FASTA and FASTQ files
  ☆71Updated 3 months ago
• moshi4 / phyTreeViz
  Simple phylogenetic tree visualization python package for phylogenetic analysis
  ☆50Updated 10 months ago
• chanzuckerberg / czid-workflows
  Portable WDL workflows for CZ ID production pipelines
  ☆47Updated last month
• bobeobibo / phigaro
  Phigaro is a scalable command-line tool for predicting phages and prophages
  ☆52Updated last year