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Related Concept Videos

Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Phylogeny01:23

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

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A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Mixed integer linear programming for maximum-parsimony phylogeny inference.

Srinath Sridhar1, Fumei Lam, Guy E Blelloch

  • 1Computer Science Department, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA. srinath@cs.cmu.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|August 2, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces two integer linear programming (ILP) methods for reconstructing phylogenetic trees from variation data. These new computational biology approaches efficiently find the most parsimonious tree, offering optimal results.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Phylogenetic tree reconstruction is crucial for understanding evolutionary relationships.
  • Existing heuristic methods face challenges with rapidly growing variation data.
  • Advances in phylogeny inference are needed for modern biological datasets.

Purpose of the Study:

  • To develop novel computational methods for reconstructing the most parsimonious phylogenetic trees.
  • To address the limitations of current heuristic approaches with large-scale variation data.
  • To provide efficient and provably optimal solutions for phylogeny inference.

Main Methods:

  • Developed two integer linear programming (ILP) formulations for maximum parsimony phylogeny inference.
  • Implemented a flow-based ILP formulation, efficient in practice despite worst-case exponential complexity.
  • Proposed an alternative formulation solvable with a polynomial-sized ILP.

Main Results:

  • The flow-based ILP method solved large mtDNA and Y-chromosome datasets rapidly, yielding provably optimal phylogenies.
  • The approach demonstrated competitive performance against heuristic methods lacking optimality guarantees.
  • A web server utilizing the exponential-sized ILP was developed for fast phylogenetic inference.

Conclusions:

  • Integer linear programming offers a powerful framework for optimal phylogenetic tree reconstruction.
  • The presented ILP methods enhance the ability to analyze large-scale biological variation data.
  • The developed web server facilitates access to efficient phylogeny inference and precomputed datasets.