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Moreover, alignment-free methods become crucial for data types like genome skims, where assembly is impractical. However, despite these benefits, alignment-free techniques have not gained widespread acceptance since they lack the accuracy of alignment-based techniques, primarily due to their reliance on simplified models of pairwise distance calculation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Here, we present a likelihood based alignment-free technique for phylogenetic tree construction. We encode the presence or absence of\n                      <jats:italic>k<\/jats:italic>\n                      -mers in genome sequences in a binary matrix, and estimate phylogenetic trees using a maximum likelihood approach. A likelihood based alignment-free method for phylogeny estimation is implemented for the first time in a software named\n                      <jats:sc>Peafowl<\/jats:sc>\n                      , which is available at:\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/github.com\/hasin-abrar\/Peafowl-repo\" ext-link-type=\"uri\">https:\/\/github.com\/hasin-abrar\/Peafowl-repo<\/jats:ext-link>\n                      . We analyze the performance of our method on seven real datasets and compare the results with the state of the art alignment-free methods.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Results suggest that our method is competitive with existing alignment-free tools. This indicates that maximum likelihood based alignment-free methods may in the future be refined to outperform alignment-free methods relying on distance calculation as has been the case in the alignment-based setting.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-025-06080-w","type":"journal-article","created":{"date-parts":[[2025,3,7]],"date-time":"2025-03-07T06:00:59Z","timestamp":1741327259000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["An alignment-free method for phylogeny estimation using maximum likelihood"],"prefix":"10.1186","volume":"26","author":[{"given":"Tasfia","family":"Zahin","sequence":"first","affiliation":[]},{"given":"Md. 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