Related Experiment Video
Updated: Dec 8, 2025
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
16.3K
Netcombin: An algorithm for constructing optimal phylogenetic network from rooted triplets
Hadi Poormohammadi1,2, Mohsen Sardari Zarchi1
1Department of Computer Engineering, Meybod University, Meybod, Iran.
Plos One
|September 18, 2020
Summary
Netcombin is a novel algorithm for constructing phylogenetic networks, which represent complex evolutionary events. It efficiently builds an approximately optimal rooted network from triplets, outperforming existing methods in speed and precision.
Area of Science:
- Phylogenetics and evolutionary biology.
- Computational biology and bioinformatics.
Background:
- Phylogenetic network construction is crucial for understanding complex evolutionary events like gene flow and hybridization.
- Rooted phylogenetic networks explicitly represent evolutionary histories but constructing optimal ones from triplets is NP-hard.
Purpose of the Study:
- Introduce Netcombin, a new algorithm for approximately optimal rooted phylogenetic network construction.
- Address the challenge of minimizing reticulation nodes and network level in phylogenetic network design.
Main Methods:
- Netcombin employs a binarization process to create a rooted tree consistent with maximum input triplets.
- An expansion process then heuristically adds edges to minimize reticulation nodes.
- The algorithm's performance is evaluated against RPNCH, NCHB, TripNet, and SIMPLISTIC using simulated data.
Main Results:
- Netcombin demonstrates superior performance compared to state-of-the-art algorithms.
- The algorithm achieves a favorable trade-off between computational speed and accuracy.
- Experimental results on simulated data confirm its effectiveness.
Conclusions:
- Netcombin offers an efficient and effective approach for constructing approximately optimal rooted phylogenetic networks.
- The algorithm's innovative binarization and expansion processes contribute to its improved performance.
- Netcombin represents a significant advancement in phylogenetic network construction methodologies.
Related Concept Videos
03:21Phylogenetic Trees
48.9K
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.
48.9K
02:54Evolutionary Relationships through Genome Comparisons
6.7K
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...
6.7K
01:23Phylogeny
56.3K
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 kingdom.
56.3K
01:24Sequence Networks of Rotating Machines
404
A Y-connected synchronous generator, grounded through a neutral impedance, is designed to produce balanced internal phase voltages with only positive-sequence components. The generator's sequence networks include a source voltage that is exclusively in the positive-sequence network. The sequence components of line-to-ground voltages at the generator terminals illustrate this configuration.
Zero-sequence current induces a voltage drop across the generator's neutral impedance and other...
Zero-sequence current induces a voltage drop across the generator's neutral impedance and other...
404
01:15Construction of Root Locus
278
The construction of a root locus involves several key steps to analyze and visualize the behavior of a system's poles with varying gain. The number of branches in the root locus equals the number of closed-loop poles and is symmetrical about the real axis.
For positive gain values, the root locus exists on the real axis to the left of an odd number of finite open-loop poles or zeros. The root locus starts at the open-loop poles and traces the paths of the closed-loop poles as the gain...
For positive gain values, the root locus exists on the real axis to the left of an odd number of finite open-loop poles or zeros. The root locus starts at the open-loop poles and traces the paths of the closed-loop poles as the gain...
278
02:27Trihybrid Crosses
24.9K
Trihybrid Crosses
Some of Mendel’s crosses examined three pairs of contrasting characteristics. Such a cross is called a trihybrid cross. A trihybrid cross is a combination of three individual monohybrid crosses. For example, plant height (tall vs. short), seed shape (round vs. wrinkled), and seed color (yellow vs. green).
The F1 generation plants of a trihybrid cross are heterozygous for all three traits and produce eight gametes. Upon self-fertilization, these gametes have an equal...
Some of Mendel’s crosses examined three pairs of contrasting characteristics. Such a cross is called a trihybrid cross. A trihybrid cross is a combination of three individual monohybrid crosses. For example, plant height (tall vs. short), seed shape (round vs. wrinkled), and seed color (yellow vs. green).
The F1 generation plants of a trihybrid cross are heterozygous for all three traits and produce eight gametes. Upon self-fertilization, these gametes have an equal...
24.9K