Computational pangenomics is an emerging research field that is changing the way
computer scientists are facing challenges in biological sequence analysis. In past decades …

Indexing highly repetitive texts—such as genomic databases, software repositories and
versioned text collections—has become an important problem since the turn of the …

Abstract Gagie, Navarro and Prezza's r-index (SODA, 2018) promises to speed up DNA
alignment and variation calling by allowing us to index entire genomic databases, provided …

Since 1977, when Lempel and Ziv described a kind of string factorization useful for text
compression, there has been a succession of algorithms proposed for computing “LZ …

Indexing highly repetitive strings (ie, strings with many repetitions) for fast queries has
become a central research topic in string processing, because it has a wide variety of …

Computing the LZ factorization (or LZ77 parsing) of a string is a computational bottleneck in
many diverse applications, including data compression, text indexing, and pattern discovery …

Constructing the suffix array for a string collection is an important task that may be performed
by sorting the concatenation of all strings. In this article we present algorithms g SAIS and g …

We consider full text index construction in external memory (EM). Our first contribution is an
inducing algorithm for suffix arrays in external memory, which runs in sorting complexity …

We show how to modify the linear-time construction algorithm for suffix arrays based on
induced sorting (Nong et al., DCC'09) such that it computes the array of longest common …

The weighted ancestor problem is a well-known generalization of the predecessor problem
to trees. It is known to require $\Omega (\log\log n) $ time for queries provided $ O (n\mathop …