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Journal Articles NAR Genomics and Bioinformatics Year : 2021

Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows

Abstract

Phylogenetics is nowadays at the center of numerous studies in many fields, ranging from comparative genomics to molecular epidemiology. However, phylogenetic analysis workflows are usually complex and difficult to implement, as they are often composed of many small, reccuring, but important data manipulations steps. Among these, we can find file reformatting, sequence renaming, tree re-rooting, tree comparison, bootstrap support computation, etc. These are often performed by custom scripts or by several heterogeneous tools, which may be error prone, uneasy to maintain and produce results that are challenging to reproduce. For all these reasons, the development and reuse of phylogenetic workflows is often a complex task. We identified many operations that are part of most phylogenetic analyses, and implemented them in a toolkit called Gotree/Goalign. The Gotree/Goalign toolkit implements more than 120 user-friendly commands and an API dedicated to multiple sequence alignment and phylogenetic tree manipulations. It is developed in Go, which makes executables easily installable, integrable in workflow environments, and parallelizable when possible. Moreover, Go is a compiled language, which accelerates computations compared to interpreted languages. This toolkit is freely available on most platforms (Linux, MacOS and Windows) and most architectures (amd64, i386) on GitHub at https://github.com/evolbioinfo/gotree, Bioconda and DockerHub.
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pasteur-03427582 , version 1 (14-11-2021)

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Frédéric Lemoine, Olivier Gascuel. Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows. NAR Genomics and Bioinformatics, 2021, 3 (3), pp.lqab075. ⟨10.1093/nargab/lqab075⟩. ⟨pasteur-03427582⟩
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