Review of: Galled Perfect Transfer Networks. Round#1/Reviewer#1

Consider character data describing traits that are each acquired exactly once, always inherited by vertical descendants, and that can be transferred by horizontal transfers.Such character data can always be explained by any rooted phylogenetic tree with added horizontal transfer events, but a large number of events may be needed [1].A major open problem is whether it is possible to efficiently find a network with a minimum number of horizontal events.Another approach is to search for a network with topological restrictions, such as galled trees (level-1 networks).Surprisingly, the problem becomes polynomial-time solvable when restricted to galled trees (both when the base tree is fixed and when it is not), as shown by Lpez Snchez and Lafond [2].I strongly recommend their paper since it clearly explains and motivates these natural problems, and clearly describes how to solve them.Although this is highly nontrivial, the clear exposition in the paper, first focusing on the high-level ideas and then filling in the details, makes it relatively easy to understand.In addition, the paper studies practical data and lists many interesting questions that remain open.

Publication Details

Journal
Peer Community In Mathematical and Computational Biology
Published
2024-11-14
DOI
https://doi.org/10.24072/pci.mcb.100395.rev11
Primary Topic
Algorithms and Data Compression
Type
article
Field-Weighted Citation Impact
0.00
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article

Review of: Galled Perfect Transfer Networks. Round#1/Reviewer#1

Peer Community In Mathematical and Computational Biology
Algorithms and Data Compression
article

Review of: Galled Perfect Transfer Networks. Round#1/Reviewer#1

article en

Abstract

Consider character data describing traits that are each acquired exactly once, always inherited by vertical descendants, and that can be transferred by horizontal transfers.Such character data can always be explained by any rooted phylogenetic tree with added horizontal transfer events, but a large number of events may be needed [1].A major open problem is whether it is possible to efficiently find a network with a minimum number of horizontal events.Another approach is to search for a network with topological restrictions, such as galled trees (level-1 networks).Surprisingly, the problem becomes polynomial-time solvable when restricted to galled trees (both when the base tree is fixed and when it is not), as shown by Lpez Snchez and Lafond [2].I strongly recommend their paper since it clearly explains and motivates these natural problems, and clearly describes how to solve them.Although this is highly nontrivial, the clear exposition in the paper, first focusing on the high-level ideas and then filling in the details, makes it relatively easy to understand.In addition, the paper studies practical data and lists many interesting questions that remain open.

Peer Community In Mathematical and Computational Biology
Openalex Percentile: Top 72%
Algorithms and Data Compression
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