{"doi":"10.1101/2021.06.09.447704","title":"Gotree/Goalign : Toolkit and Go API to facilitate the development of phylogenetic workflows","abstract":"<jats:title>ABSTRACT</jats:title>\n                <jats:p>\n                  Besides computer intensive steps, phylogenetic analysis workflows are usually 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 efficient, easily installable, integrable in workflow environments, and parallelizable when possible. This toolkit is freely available on most platforms (Linux, MacOS and Windows) and most architectures (amd64, i386). Sources and binaries are available on GitHub at\n                  <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"https://github.com/evolbioinfo/gotree\">https://github.com/evolbioinfo/gotree</jats:ext-link>\n                  , Bioconda, and DockerHub.\n                </jats:p>","journal":null,"year":null,"id":624066,"datarank":0.7076349574434935,"base_score":2.8903717578961645,"endowment":2.8903717578961645,"self_citation_contribution":0.4335557636844247,"citation_network_contribution":0.27407919375906875,"self_endowment_contribution":0.4335557636844247,"citer_contribution":0.27407919375906875,"corpus_percentile":null,"corpus_rank":null,"citation_count":17,"citer_count":15,"citers_with_citation_signal":12,"citers_with_endowment":12,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":7395,"name":"Olivier Gascuel","orcid":"0000-0002-9412-9723","position":1,"is_corresponding":false},{"id":560702,"name":"Frédéric Lemoine","orcid":"0000-0001-9576-4449","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Gotree/Goalign : Toolkit and Go API to facilitate the development of phylogenetic workflows","abstract":"<jats:title>ABSTRACT</jats:title>\n                <jats:p>\n                  Besides computer intensive steps, phylogenetic analysis workflows are usually 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 efficient, easily installable, integrable in workflow environments, and parallelizable when possible. This toolkit is freely available on most platforms (Linux, MacOS and Windows) and most architectures (amd64, i386). Sources and binaries are available on GitHub at\n                  <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"https://github.com/evolbioinfo/gotree\">https://github.com/evolbioinfo/gotree</jats:ext-link>\n                  , Bioconda, and DockerHub.\n                </jats:p>","is_dataset_classified":null,"base_score":2.8903717578961645,"endowment":2.8903717578961645,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"19767382","pmcid":null,"openalex_id":"https://openalex.org/W3166841618","authors":[],"funders":[{"funder_name":"French National Research Agency (ANR)","grant_id":"ANR-19-P3IA-0001","title":null}],"total_grants":1,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[{"year":2021,"count":2},{"year":2022,"count":5},{"year":2023,"count":2},{"year":2024,"count":4},{"year":2025,"count":4}],"oa_status":"green","license":"cc-by-nc-nd","oa_locations":[{"url":"https://www.biorxiv.org/content/biorxiv/early/2021/06/10/2021.06.09.447704.full.pdf","host_type":"repository"},{"url":"https://www.biorxiv.org/content/biorxiv/early/2021/06/10/2021.06.09.447704.full.pdf","host_type":"repository"},{"url":"https://syndication.highwire.org/content/doi/10.1101/2021.06.09.447704","host_type":"publisher"},{"url":"https://doi.org/10.1101/2021.06.09.447704","host_type":"repository"},{"url":"https://doi.org/10.1093/nargab/lqab075","host_type":""},{"url":"https://academic.oup.com/nargab/article-pdf/3/3/lqab075/40346661/lqab075.pdf","host_type":""},{"url":"https://pubmed.ncbi.nlm.nih.gov/34396097","host_type":""},{"url":"http://dx.doi.org/10.1093/nargab/lqab075","host_type":""},{"url":"https://dx.doi.org/10.1093/nargab/lqab075","host_type":""},{"url":"https://dx.doi.org/10.1101/2021.06.09.447704","host_type":""},{"url":"https://pasteur.hal.science/pasteur-03427582v1/document","host_type":""},{"url":"https://pasteur.hal.science/pasteur-03427582v1","host_type":""}],"fields_of_study":["Genomics and Phylogenetic Studies","Evolution and Paleontology Studies","Species Distribution and Climate Change","0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":[],"keywords":["Executable","Workflow","Computer science","Scripting language","Phylogenetic tree","Tree (set theory)","Reuse","Task (project management)","Programming language","Software engineering","Database","Biology","Application Notes","[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Industry, innovation and infrastructure"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-04T02:30:35.147577Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}