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RelatedMaterial
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create: {"material_type"=>"Article", "availability"=>nil, "link"=>"https://doi.org/10.1186/s13015-023-00230-6", "uri"=>"10.1186/s13015-023-00230-6", "uri_type"=>"DOI", "citation"=>"Liu, B., Warnow, T. Weighted ASTRID: fast and accurate species trees from weighted internode distances. Algorithms Mol Biol 18, 6 (2023). https://doi.org/10.1186/s13015-023-00230-6", "dataset_id"=>2101, "selected_type"=>"Article", "datacite_list"=>"IsSupplementTo"}
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2023-07-31T14:19:08Z
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Dataset
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update: {"version_comment"=>[nil, ""], "subject"=>[nil, "Life Sciences"]}
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2021-11-11T20:04:14Z
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Dataset
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update: {"title"=>["Data from \"Scalable Species Tree Inference with External Constraints\"", "Data from Scalable Species Tree Inference with External Constraints"]}
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2021-11-11T18:49:13Z
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Dataset
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update: {"description"=>["This dataset contains re-estimated gene trees from the ASTRAL-II [1] simulated datasets. The re-estimated variants of the datasets are called MC6H and MC11H -- they are derived from the MC6 and MC11 conditions from the original data (the MC1 and MC11 names are given by ASTRID [2]). The uploaded files contain the sequence alignments (half-length their original alignments), and the re-estimated species trees using FastTree2.\r\n\r\nNote:\r\n - \"mc6h.tar.gz\" and \"mc11h.tar.gz\" contain the sequence alignments and the re-estimated gene trees for the two conditions\r\n - the sequence alignments are in the format \"all-genes.phylip.splitted.[i].half\" where i means that this alignment is for the i-th alignment of the original dataset, but truncating the alignment halving its length\r\n - \"g1000.trees\" under each replicate contains the newline-separated re-estimated gene trees. The gene trees were estimated from the above described alignments using FastTree2 (version 2.1.11) command \"FastTree -nt -gtr\"\r\n\r\n[1]: Mirarab, S., & Warnow, T. (2015). ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics, 31(12), i44-i52.\r\n[2]: Vachaspati, P., & Warnow, T. (2015). ASTRID: accurate species trees from internode distances. BMC genomics, 16(10), 1-13.", "This dataset contains re-estimated gene trees from the ASTRAL-II [1] simulated datasets. The re-estimated variants of the datasets are called MC6H and MC11H -- they are derived from the MC6 and MC11 conditions from the original data (the MC6 and MC11 names are given by ASTRID [2]). The uploaded files contain the sequence alignments (half-length their original alignments), and the re-estimated species trees using FastTree2.\r\n\r\nNote:\r\n - \"mc6h.tar.gz\" and \"mc11h.tar.gz\" contain the sequence alignments and the re-estimated gene trees for the two conditions\r\n - the sequence alignments are in the format \"all-genes.phylip.splitted.[i].half\" where i means that this alignment is for the i-th alignment of the original dataset, but truncating the alignment halving its length\r\n - \"g1000.trees\" under each replicate contains the newline-separated re-estimated gene trees. The gene trees were estimated from the above described alignments using FastTree2 (version 2.1.11) command \"FastTree -nt -gtr\"\r\n\r\n[1]: Mirarab, S., & Warnow, T. (2015). ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics, 31(12), i44-i52.\r\n[2]: Vachaspati, P., & Warnow, T. (2015). ASTRID: accurate species trees from internode distances. BMC genomics, 16(10), 1-13."]}
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2021-11-03T19:08:10Z
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