Search Results for "suffix tree"
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Showing 13 open source projects for "suffix tree"
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sled
The champagne of beta embedded databases
...Zstd compression (use the compression build feature, disabled by default). Cpu-scalable lock-free implementation. Flash-optimized log-structured storage. Uses modern b-tree techniques such as prefix encoding and suffix truncation for reducing the storage costs of long keys with shared prefixes. If keys are the same length and sequential then the system can avoid storing 99%+ of the key data in most cases, essentially acting like a learned index. sled performs prefix encoding on long keys with similar prefixes that are grouped together in a range, as well as suffix truncation to further reduce the indexing costs of long keys. -
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levin
in-memory key value server with fuzzy search capabilities
Levin is an event-based key/value server based on radix-tree (space optimized trie). Key search can be performed with an approximate key matching algorithm based on Levenshtein edit distance. -
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spark-msna
Algorithm on Spark for aligning multiple similar DNA/RNA sequences
The algorithm uses suffix tree for identifying common substrings and uses a modified Needleman-Wunsch algorithm for pairwise alignments. In order to improve the efficiency of pairwise alignments, an unsupervised learning based on clustering technique is used to create a knowledge base to guide them. -
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hakmer
Parses genome sequences into k-mers for phylogeny reconstruction
This code is a homology-aware phylogenomics tool for rapidly parsing whole genome sequences and building sets of small multiple sequence alignments for tree construction. The code relies on a new implementation of suffix arrays to store and retrieve orthologous k-mers across several genomes. Resulting k-mer blocks can then be combined into one or more supermatrices for further phylogenetic analysis. -
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SplitMEM
Graphical pan-genome analysis with suffix skips
...Here we introduce a novel O(n log n) time and space algorithm called splitMEM, that directly constructs the compressed de Bruijn graph for a pan-genome of total length n. To achieve this time complexity, we augment the suffix tree with suffix skips, a new construct that allows us to traverse several suffix links in constant time, and use them to efficiently decompose maximal exact matches (MEMs) during a suffix tree traversal. -
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Suffix Grove
Suffix Grove: Genome Sequence Assembly by Suffix Tree Branch Extension
Suffix Grove is a genome sequence assembler that employs a novel algorithm based on suffix trees. It is designed to demonstrate the utility of the algorithm and is not suited to full-scale assembly efforts. -
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miniMerge
Perfect build tool for JS/CSS apps. Pure java, generic and powerful.
MiniMerge - "Merge files with dependencies." ================================================================================ Summary MiniMerge allows easy files merging with its dependencies in a defined order. It is lightweight and written purely in java. Program is a great concatenating tool, especially when used for web development build systems. It allows simply and efficiently merging JS or CSS dependencies trees into single output files. Debug web pages can be easily... -
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RuzzleSolver
Takes in a ruzzle input and solves it
...Runs a DFS on the Ruzzle grid and at each instance checks if the word formed is a valid one. 2. Since the size of a grid is just 4 x 4, optimizations (such as using a suffix tree) aren't that important. 3. The total list of possible words is obtained fairly quickly. Less than 10 seconds on an i7 machine (without using any form of parallelization or multithreading). 4. The TWL06 wordlist, same as the one used by Ruzzle, is used as the dictionary. 5. The automated swiping is done by controlling the mouse pointer and getting it to move around automatically. ... -
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MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.
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SuperWillow is a Music Generation program. Artists have many influences which they have accumulated over the years by listening to countless pieces of music, this principle is reflected in SuperWillow.
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The gsuffix library implements serveral algorithms used for enumerative string searches. It incorporates the suffix tree and suffix array data structures as well as some other methods.
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lcslib is a free library intended for finding longest common substrings in byte strings. It implements structure of suffix tree that is highly optimized for 256-character alphabet. It was originally implemented for finding signatures in TCP dumps.
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A Java API for using suffix trees with natural language and an Eclipse/SWT-based GUI for suffix tree visualization using Graphviz.
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