Mathematical software

STXXL
Referenced in 18 articles [sw06824]
components, breadth-first search decompositions, constructing suffix arrays, and computing social network analysis metrics...

STAR
Referenced in 14 articles [sw02515]
maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure...

libdivsufsort
Referenced in 3 articles [sw38865]
software library that implements a lightweight suffix array construction algorithm. This library provides a simple ... efficient C API to construct a suffix array and a Burrows-Wheeler transformed string from...

mkESA
Referenced in 2 articles [sw35130]
mkESA: enhanced suffix array construction tool. Summary: We introduce the tool mkESA, an open source ... program for constructing enhanced suffix arrays (ESAs), striving for low memory consumption, yet high practical ... parallelized version of the Deep-Shallow suffix array construction algorithm, which is known ... files with multiple sequences, and computes suffix arrays and various additional tables, such...

Big-BWT
Referenced in 3 articles [sw34744]
build the BWT and optionally the Suffix Array for highly repetitive files using the approach...

Fiona
Referenced in 3 articles [sw34360]
efficient implementation of the partial suffix array to detect read overlaps with different seed lengths...

RAPSearch2
Referenced in 3 articles [sw23045]
suffix array data structure. Here we present RAPSearch2, a new memory-efficient implementation...

IGTools
Referenced in 3 articles [sw34225]
main goal of IGTools, where suffix arrays are a key point in the data structures...

GSNAP
Referenced in 1 article [sw17306]
than four billion bp, and enhanced suffix arrays (ESAs) with novel data structures for fast ... greedy match-and-extend algorithm using suffix arrays, segment chaining using genomic hash tables, diagonalization...

KABOOM
Referenced in 1 article [sw35129]
KABOOM! A new suffix array based algorithm for clustering expression data. Results: We introduce ... efficient implementation using modified suffix arrays. We demonstrate its efficiency by presenting our new expression...

STXXL