{"doi":"10.1093/molbev/msm092","title":"MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0","abstract":"We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multi-user supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at (http://www.megasoftware.net).","journal":"Molecular Biology and Evolution","year":2007,"id":515,"datarank":22.542758775450793,"base_score":10.26670604071587,"endowment":10.26670604071587,"self_citation_contribution":1.5400059061073808,"citation_network_contribution":21.00275286934341,"self_endowment_contribution":1.5400059061073808,"citer_contribution":21.00275286934341,"corpus_percentile":96.66395443449959,"corpus_rank":42,"citation_count":28811,"citer_count":197,"citers_with_citation_signal":197,"citers_with_endowment":197,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6768,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2007-04-18","fair_score":27.9167,"fair_percentile":8.839050131926122,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":5154,"name":"M. Nei","orcid":null,"position":2,"is_corresponding":false},{"id":3955,"name":"Koichiro Tamura","orcid":"0000-0001-7189-5399","position":4,"is_corresponding":false},{"id":48,"name":"Joel T. Dudley","orcid":"0000-0002-7036-6492","position":5,"is_corresponding":false},{"id":3959,"name":"Sudhir Kumar","orcid":"0000-0002-9918-8212","position":6,"is_corresponding":false}],"reference_count":9,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","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":32.0,"fair_a":58.0,"fair_i":5.0,"fair_r":16.6667,"fair_zscore":-1.5644,"fair_rationale":{"fair_score":27.92,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":32.0,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"datacite=0, pmcid=False, pmid=False","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.0,"signal":null,"rationale":"No evidence of rich, machine-readable metadata such as structured descriptions or formal metadata schemas; the paper provides only natural language summaries."}]},"A":{"name":"Accessible","score":58.0,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"The software is freely available at a URL, but there is no explicit description of a protocol for accessing the underlying data or code (e.g., repository, versioning, or persistent identifier)."}]},"I":{"name":"Interoperable","score":5.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.25,"signal":null,"rationale":"The paper mentions standard biological data types (e.g., DNA sequences, phylogenetic trees) but does not explicitly state use of controlled vocabularies, standard formats (e.g., FASTA, Newick), or unique identifiers."}]},"R":{"name":"Reusable","score":16.67,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.167,"signal":null,"rationale":"No data-availability statement, license for the software, or explicit reproducibility mechanisms are provided; only a download URL and brief usage notes are given."}]}},"suggestions":["Include structured metadata (e.g., schema.org or DataCite) with persistent identifiers for the software and associated datasets.","Provide a formal data-access protocol, such as a DOI, repository link, and explicit instructions for accessing underlying test data.","Use standard file formats for input/output (e.g., FASTA, Newick, Nexus) and reference controlled vocabularies (e.g., EDAM ontology).","Add a data-availability statement, license (e.g., GNU GPL), and reproducibility details (e.g., example run scripts and output)."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"abstract_only"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"abstract_only","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:23:12.555511Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}