kasravnd / SuffixTree
Optimized implementation of suffix tree in python using Ukkonen's algorithm.
☆51Updated 2 years ago
Alternatives and similar repositories for SuffixTree:
Users that are interested in SuffixTree are comparing it to the libraries listed below
- Python implementation of Suffix Trees and Generalized Suffix Trees.☆126Updated 4 years ago
- Suffix tree for string searching☆160Updated 3 years ago
- A Generalized Suffix Tree for any Python iterable using Ukkonen's algorithm, with Lowest Common Ancestor retrieval.☆51Updated last year
- Ukkonen's suffix tree algorithm, a complete version implemented in Python☆26Updated last year
- C++ implementation of FM Index data structure wrapped in Python☆13Updated 2 years ago
- cython wrapper for khash☆29Updated 10 months ago
- Parallel Suffix Array, LCP Array, and Suffix Tree Construction☆49Updated 5 years ago
- Fast hierarchical clustering routines for R and Python.☆144Updated this week
- A package for combining multiple partitions into a consolidated clustering. The combinatorial optimization problem of obtaining such a co…☆70Updated 2 years ago
- Practical Dynamic de Bruijn Graphs☆18Updated 4 years ago
- Succinct Data Structure Library☆106Updated 11 years ago
- FM-Index full-text index implementation using RRR Wavelet trees (libcds) and fast suffix sorting (libdivsufsort) including experimental r…☆108Updated 10 years ago
- Minhash and maxhash library in Python, combining flexibility, expressivity, and performance.☆21Updated 4 months ago
- SNP Extraction Tool for Human Variations☆27Updated last year
- dna2vec: Consistent vector representations of variable-length k-mers☆184Updated 2 years ago
- fast, pure-python interval overlap testing☆52Updated 4 years ago
- A collection of Python scripts that implement various graph clustering algorithms, specifically for identifying protein complexes from pr…☆94Updated 6 years ago
- Algorihms about Suffix Array Construction, Suffix Tree, Longest Common Prefix, Burrows Wheeler Transform,☆12Updated 5 years ago
- The Nested Containment List for Python. Basically a static interval-tree that is silly fast for both construction and lookups.☆220Updated 7 months ago
- Open compressed files in Python☆73Updated 2 weeks ago
- Find parts of long text or data, allowing for some changes/typos.☆319Updated 8 months ago
- Preparing DMOZ dataset for my n-Gram LM-based URL classification research☆32Updated 10 years ago
- Linked list extension module for Python☆79Updated 7 months ago
- 💥 Cython hash tables that assume keys are pre-hashed☆87Updated 3 months ago
- linear (time,space) greedy set cover implementation☆30Updated 3 years ago
- Generation of CWL programmatically. Available types: CommandLineTool and DockerRequirement☆29Updated 4 years ago
- A tool for merging large BWTs☆26Updated 4 years ago
- ☆81Updated last month
- graph-tool - Efficient network analysis☆101Updated last year
- FM-index representation of a de Bruijn graph☆27Updated 7 years ago