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In this work we present a comparative analysis of seven automated reconstruction tools (AuReMe, CarveMe, merlin, ModelSEED, Pathway Tools, RAVEN and Reconstructor) applied to three multicellular eukaryotes: the mosquito\n                    <jats:italic>Aedes aegypti<\/jats:italic>\n                    , the CHO (Chinese Hamster Ovary) cell line from\n                    <jats:italic>Cricetulus griseus<\/jats:italic>\n                    and the brown algae\n                    <jats:italic>Ectocarpus siliculosus<\/jats:italic>\n                    . Evaluation of these tools was based on metrics for network size, functionality, consistency, representation of organelle-specific functions and organism-specific metabolites, annotation quality and execution time. We find that methods differ strongly in a trade-off between model functionality and representation of eukaryotic features such as compartmentalization and organism-specific metabolism, with no single approach excelling at both. Our work aims at providing a practical resource to guide researchers in selecting methods for draft generation tailored to organism characteristics and research goals.\n                  <\/jats:p>","DOI":"10.1186\/s12859-026-06455-7","type":"journal-article","created":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T17:12:47Z","timestamp":1779469967000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Selecting methods for draft GEM generation in multicellular eukaryotes: a comparative analysis"],"prefix":"10.1186","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2084-1256","authenticated-orcid":false,"given":"Natalia E.","family":"Jim\u00e9nez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mikael","family":"Espinoza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebasti\u00e1n","family":"Mej\u00edas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2192-5569","authenticated-orcid":false,"given":"Sebasti\u00e1n N.","family":"Mendoza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ignacia","family":"Segovia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. 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