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MOTIVATION The Illumina paired-end sequencing technology can generate reads from both ends of target DNA fragments, which can subsequently be merged to increase the overall read length. There already exist tools for merging these paired-end reads when the target fragments are equally long. However, when fragment lengths vary and, in particular, when either(More)
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically(More)
A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of mismatches in the alignment; however, their(More)
BACKGROUND VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily(More)
— With Next Generation Sequencing Data (NGS) coming off age and being routinely used, evolutionary biology is transforming into a data-driven science. As a consequence, researchers have to rely on a growing number of increasingly complex software. All widely used tools in our field have grown considerably, in terms of the number of features as well as lines(More)
  • Nikolai Baudis, Pierre Barbera, Sebastian Graf, Sarah Lutteropp, Daniel Opitz, Tomáš Flouri +1 other
  • 2015
In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology , we developed and make available two independent and highly optimized open-source implementations for the pair-wise statistical alignment model, also known as TKF91, that was developed by Thorne, Kishino, and Felsenstein in(More)
Pairwise sequence alignment is perhaps the most fundamental bioinformatics operation. An optimal global alignment algorithm was described in 1970 by Needleman and Wunsch. In 1982 Gotoh presented an improved algorithm with lower time complexity. Gotoh's algorithm is frequently cited (1447 citations, Google Scholar, May 2015), taught and, most importantly,(More)
Background: A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of mismatches in the alignment; however,(More)
— The Pattern Matching problem with swaps is a variation of the classical pattern matching problem. It consists of finding all the occurrences of a pattern P in a text T , when an unrestricted number of disjoint local swaps is allowed. In this paper, we present a new, efficient method for the Swap Matching problem with short patterns. In particular, we(More)
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