Alternatives and similar repositories for clusty

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

• AllTheBacteria / Phylign
  Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…
  ☆12Updated last year
• pg-space / panspace
  Embedding-based indexing for compact storage, rapid querying, and curation of bacterial pan-genomes
  ☆12Updated 2 months ago
• bo1929 / krepp
  A k-mer-based maximum likelihood method for estimating distances of reads to genomes and phylogenetic placement.
  ☆16Updated 3 weeks ago
• JMencius / LongBow
  Basecalling configuration prediction through FASTQ files
  ☆23Updated 4 months ago
• althonos / pyskani
  PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
  ☆26Updated last month
• fpusan / SuperPang
  Non-redundant pangenome assemblies from multiple genomes or bins
  ☆13Updated 4 months ago
• kangxiongbin / HyLight
  HyLight is a strain aware de novo assembly method based on the overlap-layout-consensus (OLC) paradigm that leverages the strengths of NG…
  ☆12Updated last year
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆20Updated 8 months ago
• bluenote-1577 / devider
  Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs
  ☆31Updated last week
• lrobidou / KFC
  ☆18Updated 7 months ago
• gcgreenberg / LexicHash
  A novel method for sequence similarity estimation
  ☆28Updated last year
• rrwick / Are-reads-required
  ☆10Updated 4 months ago
• at-cg / mm2-plus
  Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)
  ☆35Updated 3 months ago
• althonos / pyfastani
  Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
  ☆22Updated last month
• TravisWheelerLab / BATH
  Better Alignments with Translated HMMER
  ☆23Updated this week
• sanger-pathogens / panito
  Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment
  ☆16Updated 6 years ago
• ekg / pafcheck
  PAF (pairwise alignment format) validator based on extended CIGAR strings
  ☆15Updated 2 months ago
• KatyBrown / plot_phylo
  Python package to plot a phylogenetic tree on an existing matplotlib axis.
  ☆25Updated 2 months ago
• fawaz-dabbaghieh / gfa_subgraphs
  Extracts subgraphs or components from a graph in GFA format
  ☆24Updated 10 months ago
• althonos / pysylph
  PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.
  ☆20Updated 9 months ago
• at-cg / PanAligner
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆39Updated last year
• Kalan-Lab / codoff
  codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, prophage, etc.) relative to the…
  ☆13Updated 3 weeks ago
• StephenHwang / MEMO
  MEMO: MEM-based pangenome indexing for k-mer queries
  ☆18Updated last year
• bioinf-mcb / MANIAC
  Computation of average nucleotide identity with the use of MMseqs2
  ☆15Updated 9 months ago
• sourmash-bio / sourmash_plugin_branchwater
  fast, multithreaded sourmash operations: search, compare, and gather.
  ☆23Updated last week
• amkram / shusher
  Private, browser-based placement of genome sequences on phylogenetic trees using UShER.
  ☆11Updated 10 months ago
• pierrepeterlongo / kmer2sequences
  Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.
  ☆21Updated last year
• wh-xu / Hyper-Gen
  HyGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors
  ☆29Updated last year
• iqbal-lab-org / cobs
  COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)
  ☆20Updated 10 months ago
• IndexThePlanet / LoganSearch
  A k-mer search engine for all Sequence Read Archive public accessions
  ☆32Updated 11 months ago