Alternatives and similar repositories for phastSim

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

• karel-brinda / Phylign
  Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
  ☆39Updated last year
• bioforensics / pytaxonkit
  Python bindings for the TaxonKit library
  ☆41Updated 4 months ago
• pirovc / multitax
  Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)
  ☆47Updated 4 months ago
• aaronmussig / PhyloDM
  Efficient calculation of phylogenetic distance matrices.
  ☆48Updated last year
• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆43Updated 7 months ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated last month
• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆44Updated 3 months ago
• salzberg-lab / Balrog
  Bacterial Annotation by Learned Representation of Genes
  ☆58Updated 4 years ago
• iqtree / piqtree
  A Python library that exposes features from IQ-TREE - efficient software for phylogenomic inference
  ☆38Updated last week
• EBI-Metagenomics / emg-toolkit
  MGnify API toolkit
  ☆19Updated 9 months ago
• unipept / FragGeneScanRs
  Better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads.
  ☆30Updated 2 months ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated 2 years ago
• PAiewsakun / GRAViTy
  ☆17Updated 3 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆56Updated 7 months ago
• steineggerlab / ufcg
  UFCG: Universal Fungal Core Genes
  ☆34Updated 3 months ago
• broadinstitute / StrainGE
  strain-level analysis tools
  ☆39Updated last year
• althonos / pyrodigal-gv
  A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.
  ☆20Updated 3 months ago
• metagentools / GraphBin2
  ☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
  ☆37Updated 3 weeks ago
• BeatsonLab-MicrobialGenomics / micropipe
  A pipeline for high-quality bacterial genome construction using ONT sequencing
  ☆39Updated 3 years ago
• PedroMTQ / mantis
  A package to annotate protein sequences
  ☆60Updated 8 months ago
• apcamargo / taxopy
  A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers
  ☆51Updated last week
• BioSina / Panakeia
  Prokaryotic Pangenome Analysis
  ☆24Updated 3 years ago
• GCA-VH-lab / FlaGs
  ☆19Updated 3 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆60Updated 2 months ago
• bluenote-1577 / fairy
  alignment-free coverage calculation for metagenomic binning >100 times faster
  ☆48Updated 8 months ago
• althonos / pyfastani
  Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
  ☆23Updated last month
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 2 months ago
• chrisquince / STRONG
  Strain Resolution ON Graphs
  ☆48Updated 2 years ago
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆51Updated last month