Browsing by Author "Di Tommaso, Paolo"

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  • Chang, Jia-Ming, 1978-; Floden, Evan Wade; Herrero, Javier; Gascuel, Olivier; Di Tommaso, Paolo; Notredame, Cedric (Oxford University Press, 2019)
    Motivation: Most evolutionary analyses are based on pre-estimated multiple sequence alignment. Wong et al. established the existence of an uncertainty induced by multiple sequence alignment when reconstructing phylogenies. ...
  • Garriga, Edgar; Di Tommaso, Paolo; Magis, Cedrik; Erb, Ionas; Mansouri, Leila; Baltzis, Athanasios; Floden, Evan, 1985-; Notredame, Cedric (Humana Press (Springer Imprint), 2021)
    Many fields of biology rely on the inference of accurate multiple sequence alignments (MSA) of biological sequences. Unfortunately, the problem of assembling an MSA is NP-complete thus limiting computation to approximate ...
  • Strozzi, Francesco; Jansenn, Roel; Wurmus, Ricardo; Crusoe, Michael R.; Githinji, George; Di Tommaso, Paolo; Belhachemi, Dominique; Möller, Steffen; Smant, Geert; de Ligt, Joep; Prins, Pjotr (Springer, 2019)
    Biological, clinical, and pharmacological research now often involves analyses of genomes, transcriptomes, proteomes, and interactomes, within and between individuals and across species. Due to large volumes, the analysis ...
  • Chang, Jia-Ming, 1978-; Di Tommaso, Paolo; Lefort, Vincent; Gascuel, Olivier; Notredame, Cedric (Oxford University Press, 2015)
    This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index. The evaluation ...
  • Di Tommaso, Paolo; Palumbo, Emilio; Chatzou, Maria, 1985-; Prieto Barja, Pablo, 1986-; Heuer, Michael L.; Notredame, Cedric (PeerJ Inc., 2015)
    Genomic pipelines consist of several pieces of third party software and, because of their experimental nature, frequent changes and updates are commonly necessary thus raising serious deployment and reproducibility issues. ...

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