The phylogenomic classification of protein sequences attempts to categorize a given protein within the evolutionary context of the entire family. It involves mainly four steps: selection of homologous sequences, multiple sequence alignment, phylogenetic tree construction and tree-based classification. This supposes that the tree used as a basis of protein classification is correct. Sequence ali...

Different species of gazelles are among the most endangered mammals on the Asian steppes and occur in the central, southern and northwestern regions of Iran. The previous conservation efforts in this region have been incomplete due to confusion about the phylogenetic relationship among various populations. So that, different conservation programs such as ex-situ breeding and transfer of captive...

For two rooted phylogenetic trees T and T ′, the rooted subtree prune and regraft distance between T and T ′ has often been used as a replacement for the hybridization number of T and T ′. However, Baroni et al. [1] constructed particular instances that showed both the difference and the ratio between this number and distance can be arbitrarily large. In this note, we show that the difference a...

We answer, in the affirmitive, the following question proposed by Mike Steel as a $100 challenge: “Is the following problem NP hard? Given a ternary phylogenetic X-tree T and a collection Q of quartet subtrees on X, is T the only tree that displays Q?” [25,27]

The composition vector (CV) method is an alignment-free method for phylogenetics. Because of its simplicity when compared with the alignment-based methods, the method has been widely discussed lately. There are mainly four steps in the CV method: (1) count the frequency of each k-string in the sequence; (2) construct the composition vector for the sequence; (3) compute the distance between ever...

Consider two phylogenetic networks N and N ′ of size n. The tripartition-based distance finds the proportion of tripartitions which are not shared by N and N . This distance is proposed by Moret et al (2004) and is a generalization of Robinson-Foulds distance, which is orginally used to compare two phylogenetic trees. This paper gives an O(min{kn log n, n logn+ hn})-time algorithm to compute th...

The genotype phasing problem is to determine the haplotypes of diploid individuals from their genotypes where linkage relationships are not known. Based on the model of perfect phylogeny, the genotype phasing problem can be solved in linear time. However, recombinations may occur and the perfect phylogeny model thus cannot interpret genotype data with recombinations. This paper develops a graph...

In studies of molecular evolution, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For the purpose of validating evolutionary models, biologists check whether or not a phylogenetic tree (resp. cluster) is contained in a phylogenetic net...

We report on a suite of algorithms and techniques that together provide a simulation flow for studying the topological accuracy of methods for reconstructing phylogenetic networks. We implemented those algorithms and techniques and used three phylogenetic reconstruction methods for a case study of our tools. We present the results of our experimental studies in analyzing the relative performanc...