{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T12:52:38Z","timestamp":1762865558455},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The computational inference of ancestral genomes consists of five difficult steps: identifying syntenic regions, inferring ancestral arrangement of syntenic regions, aligning multiple sequences, reconstructing the insertion and deletion history and finally inferring substitutions. Each of these steps have received lot of attention in the past years. However, there currently exists no framework that integrates all of the different steps in an easy workflow. Here, we introduce Ancestors 1.0, a web server allowing one to easily and quickly perform the last three steps of the ancestral genome reconstruction procedure. It implements several alignment algorithms, an indel maximum likelihood solver and a context-dependent maximum likelihood substitution inference algorithm. The results presented by the server include the posterior probabilities for the last two steps of the ancestral genome reconstruction and the expected error rate of each ancestral base prediction.<\/jats:p>\n               <jats:p>Availability: The Ancestors 1.0 is available at http:\/\/ancestors.bioinfo.uqam.ca\/ancestorWeb\/.<\/jats:p>\n               <jats:p>Contact: \u00a0diallo.abdoulaye@uqam.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp600","type":"journal-article","created":{"date-parts":[[2009,10,23]],"date-time":"2009-10-23T01:53:19Z","timestamp":1256262799000},"page":"130-131","source":"Crossref","is-referenced-by-count":36,"title":["Ancestors 1.0: a web server for ancestral sequence reconstruction"],"prefix":"10.1093","volume":"26","author":[{"given":"Abdoulaye Banire","family":"Diallo","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al, PO. Box 8888 Downtown Station, Montreal Qc, H3C 3P8 and 2 School of Computer Science, McGill University, 3630 University street #3107, Montreal, Qc, H3A 2B2, Canada"},{"name":"1 Department of Computer Science, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al, PO. Box 8888 Downtown Station, Montreal Qc, H3C 3P8 and 2 School of Computer Science, McGill University, 3630 University street #3107, Montreal, Qc, H3A 2B2, Canada"}]},{"given":"Vladimir","family":"Makarenkov","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al, PO. Box 8888 Downtown Station, Montreal Qc, H3C 3P8 and 2 School of Computer Science, McGill University, 3630 University street #3107, Montreal, Qc, H3A 2B2, Canada"}]},{"given":"Mathieu","family":"Blanchette","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al, PO. Box 8888 Downtown Station, Montreal Qc, H3C 3P8 and 2 School of Computer Science, McGill University, 3630 University street #3107, Montreal, Qc, H3A 2B2, Canada"}]}],"member":"286","published-online":{"date-parts":[[2009,10,22]]},"reference":[{"key":"2023012507531999600_B1","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1101\/gr.1933104","article-title":"Aligning multiple genomic sequences with the threaded blockset aligner","volume":"14","author":"Blanchette","year":"2004","journal-title":"Genome Res."},{"key":"2023012507531999600_B2","doi-asserted-by":"crossref","first-page":"2412","DOI":"10.1101\/gr.2800104","article-title":"Reconstructing large regions of an ancestral mammalian genome in silico","volume":"14","author":"Blanchette","year":"2004","journal-title":"Genome Res."},{"key":"2023012507531999600_B3","first-page":"171","article-title":"Computational Reconstruction of ancestral DNA sequences, Ch. 11","volume-title":"Methods in Molecular Biology: Phylogenomics.","author":"Blanchette","year":"2008"},{"key":"2023012507531999600_B4","doi-asserted-by":"crossref","first-page":"3258","DOI":"10.1093\/bioinformatics\/btm402","article-title":"Transducers: an emerging probabilistic framework for modeling indels on trees","volume":"23","author":"Bradley","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012507531999600_B5","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1142\/S0219720006002168","article-title":"On the inference of parsimonious indel evolutionary scenarios","volume":"4","author":"Chindelevitch","year":"2006","journal-title":"J. Bioinform. Comput. Biol."},{"key":"2023012507531999600_B6","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1089\/cmb.2007.A006","article-title":"Exact and heuristics methods to indel maximum likelihood problem","volume":"14","author":"Diallo","year":"2007","journal-title":"J. Comput. Biol."},{"key":"2023012507531999600_B7","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"Multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012507531999600_B8","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-5-123","article-title":"GASP: Gapped ancestral sequence prediction for proteins","volume":"5","author":"Edwards","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023012507531999600_B9","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1007\/BF01734359","article-title":"Evolutionary trees from DNA sequences: a maximum likelihood approach","volume":"17","author":"Felsenstein","year":"1981","journal-title":"J. Mol. 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