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Everything about Tree alignment
In computational phylogenetics, tree alignment is a computational problem concerned with producing multiple sequence alignments, or alignments of three or more sequences of DNA, RNA, or protein. Sequences are arranged into a phylogenetic tree, modeling the evolutionary relationships between species or taxa. The edit distances between sequences are calculated for each of the tree's internal vertices, such that the sum of all edit distances within the tree is minimized. Tree alignment can be accomplished using one of several algorithms with various trade-offs between manageable tree size and computational effort. Wikipedia →
🧭 Start here: a 6-step reading path
- Read the overview: Tree alignmentA 5-minute orientation
- Skim a recent paper: A 3D Monte Carlo tree search method for railway alignment optimizationInfluential work since 2022
- Pick up a classic book: Assuring IT GovernanceThe most-reprinted book on the subject
- Read the landmark paper: Sensitive protein alignments at tree-of-life scale using DIAMONDCited 5,604 times
- Go sideways: Felsenstein's tree-pruning algorithmA closely related topic
- Go sideways: Graphical time warpingA closely related topic
📖 Definitions
No dictionary entry for this exact phrase.
🗂️ The subject at a glance
🏆 Landmark papers (most cited)
Sensitive protein alignments at tree-of-life scale using DIAMOND
SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building
An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty
Independence of alignment and tree search
TCS: A New Multiple Sequence Alignment Reliability Measure to Estimate Alignment Accuracy and Improve Phylogenetic Tree Reconstruction
Alignment of trees — an alternative to tree edit
Structured Data Extraction from the Web Based on Partial Tree Alignment
T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life
🆕 Influential since 2022
A 3D Monte Carlo tree search method for railway alignment optimization
Vertical alignment optimization of mountain railways with terrain-driven greedy algorithm improved by Monte Carlo tree search
Fast and accurate short-read alignment with hybrid hash-tree data structure
MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction
Fast-Evolving Alignment Sites Are Highly Informative for Reconstructions of Deep Tree of Life Phylogenies
📚 Books worth reading
Assuring IT GovernanceRobert E. Davis, MBA, CISA, CICA · 2011
Ranked by number of editions on Open Library, a rough measure of how lasting a book is.
🔗 Related topics
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- Multiple sequence alignment Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or…
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