Open AccessA LASSO-based approach to sample sites for phylogenetic tree search
Author(s) -
Noa Ecker,
Dana Azouri,
Ben Bettisworth,
Alexandros Stamatakis,
Yishay Mansour,
Itay Mayrose,
Tal Pupko
Publication year - 2022
Publication title -
bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.599
H-Index - 390
eISSN - 1367-4811
pISSN - 1367-4803
DOI - 10.1093/bioinformatics/btac252
Subject(s) - phylogenetic tree , lasso (programming language) , python (programming language) , computer science , tree (set theory) , tree rearrangement , inference , artificial intelligence , data mining , machine learning , algorithm , mathematics , biology , mathematical analysis , biochemistry , world wide web , gene , operating system
In recent years, full-genome sequences have become increasingly available and as a result many modern phylogenetic analyses are based on very long sequences, often with over 100 000 sites. Phylogenetic reconstructions of large-scale alignments are challenging for likelihood-based phylogenetic inference programs and usually require using a powerful computer cluster. Current tools for alignment trimming prior to phylogenetic analysis do not promise a significant reduction in the alignment size and are claimed to have a negative effect on the accuracy of the obtained tree.