Related Experiment Video
Updated: May 13, 2026

A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
Improvements on bicriteria pairwise sequence alignment: algorithms and applications
Maryam Abbasi1, Luís Paquete, Arnaud Liefooghe
1CISUC, Department of Informatics Engineering, University of Coimbra, Pólo II, Coimbra, Portugal.
Motivation:
In this article, we consider the bicriteria pairwise sequence alignment problem and propose extensions of dynamic programming algorithms for several problem variants with a novel pruning technique that efficiently reduces the number of states to be processed. Moreover, we present a method for the construction of phylogenetic trees based on this bicriteria framework. Two exemplary cases are discussed.
Results:
Numerical results on a real dataset show that this approach is very fast in practice. The pruning technique saves up to 90% in memory usage and 80% in CPU time. Based on this method, phylogenetic trees are constructed from real-life data. In addition of providing complementary information, some of these trees match those obtained by the Maximum Likelihood method.
Availability And Implementation:
Source code is freely available for download at URL http://eden.dei.uc.pt/paquete/MOSAL, implemented in C and supported on Linux, MAC OS and MS Windows.
More Related Videos
07:49Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
Published on: August 16, 2017
07:08Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Related Concept Videos
Evolutionary Relationships through Genome Comparisons
Applications of Molecular Taxonomy
Modern Molecular Taxonomy
Maxam-Gilbert Sequencing
Challenges of the Maxam-Gilbert Method
The...