• acss

  • Referenced in 7 articles [sw10997]
  • acss: Algorithmic Complexity for Short Strings. Main functionality is to provide the algorithmic complexity...
  • OACC

  • Referenced in 7 articles [sw10996]
  • complexity through various numerical methods and algorithms for potential applications in a very wide range ... complexity for binary strings of short length by means of algorithmic probability (notably by using ... frequency and complexity), for string length which lossless compression algorithms fail to deal with, hence ... developed called the Block Decomposition Method. More algorithmic information measures, more data and more techniques...
  • Xaa

  • Referenced in 2 articles [sw29862]
  • framework to animate string algorithms. We present an algorithm animation system, Xaa, which is tailored ... string algorithms, and, in general, to algorithms that have as input one or two dimensional...
  • ViennaRNA

  • Referenced in 22 articles [sw10504]
  • thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty et.al 1999) which generates all suboptimal ... either string alignment or tree-editing (Shapiro & Zhang 1990). Finally, we provide an algorithm...
  • S3

  • Referenced in 7 articles [sw19495]
  • symbolic string solver. Our solver employs a new algorithm for a constraint language that ... main string operations, such as those in JavaScript. The algorithm first makes ... regular expression can be encoded as string equations. Secondly, there is a constraint-based generation...
  • Biostrings

  • Referenced in 3 articles [sw14509]
  • matching algorithms. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation...
  • AquaLog

  • Referenced in 5 articles [sw23489]
  • GATE NLP platform, string metric algorithms, WordNet and a novel ontology-based relation similarity service...
  • siEDM

  • Referenced in 3 articles [sw28064]
  • siEDM: an efficient string index and search algorithm for edit distance with moves. Although several ... collections exist, developing an index and search algorithm with editing operations remains a challenge ... measure. We propose the first algorithm, named {it string index for edit distance with moves ... indexing and searching strings with EDM. The siEDM algorithm builds an index structure by leveraging...
  • StrSolve

  • Referenced in 5 articles [sw21857]
  • program analysis and testing frameworks. Stand-alone string constraint solving tools, called decision procedures, have ... this work is to provide algorithms and implementations that can be used by a variety ... separation enables independent improvement of string constraint solving algorithms and reduces client effort. We present ... decision procedure that reasons about equations over string variables. Our approach scales well with respect...
  • Readjoiner

  • Referenced in 4 articles [sw37848]
  • framework of growing interest is the assembly string graph, not necessitating a division ... reads into k-mers, but requiring fast algorithms for the computation of suffix-prefix matches ... efficient methods for the construction of a string graph from a set of sequencing reads ... suffix-prefix match determination and string graph construction algorithms have been implemented in the software...
  • Sally

  • Referenced in 2 articles [sw08470]
  • implementation of Sally builds on efficient string algorithms and enables processing millions of strings...
  • STRING

  • Referenced in 30 articles [sw23938]
  • describe the update to version 9.1 of STRING, introducing several improvements: (i) we extend ... articles; (ii) we entirely re-designed the algorithm for transferring interactions from one model organism...
  • PAMA

  • Referenced in 1 article [sw02545]
  • PAMA: a fast string matching algorithm. String matching is a fundamental operation in computer science ... this paper, we propose a fast string matching algorithm, PAMA (PAttern MAtching). The shift rule ... algorithm, but also employs an additional key observation to enable faster shifting during the string ... much as that of the Boyer-Moore algorithm. Experimentally, we show that PAMA indeed significantly...
  • PALP

  • Referenced in 70 articles [sw00672]
  • subpolytopes, and applications to toric geometry and string theory, like the computation of Hodge data ... originally intended for low-dimensional applications, the algorithms work in any dimension...
  • DISPMODULE

  • Referenced in 2 articles [sw20178]
  • Algorithm 892: DISPMODULE: a Fortran 95 module for pretty-printing matrices. A standard Fortran ... convert numerical scalars and vectors to strings...
  • libGE

  • Referenced in 2 articles [sw24012]
  • with any kind of search algorithm, translates a string of objects onto a program ... libGE is used by an evolutionary computation algorithm, providing a mapping from a genotypic structure ... maps a string provided by a variable-length genetic algorithm onto a syntactically-correct program...
  • Flamingo

  • Referenced in 2 articles [sw18861]
  • source code of several algorithms for approximate string matching developed at UC Irvine. It includes...
  • zipHMMlib

  • Referenced in 1 article [sw23251]
  • algorithm. zipHMM is a library for hidden Markov models that exploits repetitions in strings ... string - similar to how compression algorithms compresses strings - by replacing substrings with new symbols ... strings. The full likelihood can then be computed similar to the traditional forward algorithm ... much faster since the algorithm can skip over often seen strings...
  • LASSAP

  • Referenced in 3 articles [sw33234]
  • Blast, Smith/Waterman), and other string matching and pattern matching algorithms. LASSAP is both an integrated...