This investigation was aimed to compare the inference of antelope phylogenies resulting from the 16S rRNA, cytochrome-b (cyt-b) and d-loop segments of mitochondrial DNA using three different computational models including Bayesian (BA), maximum parsimony (MP) and unweighted pair group method with arithmetic mean (UPGMA). The respective nucleotide sequences of three Oryx species (Oryx leucoryx, ...

Unweighted Pair Group Method with Arithmetic Mean (UPGMA) is one of the most popular distance-based methods to reconstruct an equidistant phylogenetic tree from a distance matrix computed alignment sequences. Since we use trees as gene for phylogenomic analyses under multi-species coalescent model and since input each in genome estimated via maximum likelihood estimators, it important conduct r...

Motivation: UPGMA (average-linkage clustering) is probably the most popular algorithm for hierarchical data clustering, especially in computational biology. UPGMA however, is a complete-linkage method, in the sense that all edges between data points are needed in memory. Due to this prohibitive memory requirement UPGMA is not scalable for very large datasets. Results: We present novel memory-co...

In this work, the part of the squash core collection, maintained in the Greek Gene Bank, was assessed using the morphological and molecular data. Sixteen incompletely classified accessions of the squash were characterized along with an evaluation of their resistance against two isolates of Fusarium oxysporum. A molecular analysis using Random Amplified Polymorphic DNA (RAPD) markers was also pe...

Methods Pattern analysis of a chorological dataset, consisting of the occurrences of 3041 vascular plant species in each of the 50 km 9 50 km UTM cells of a grid covering Iberia and the Balearic Islands, was based on cluster analysis (unweighted pair-group method using arithmetic averages; UPGMA) and parsimony analysis of endemicity (PAE). The Jaccard similarity index was used in the UPGMA, and...

the aim of the present study was to find the best or optimum topology of six chicken populations, which were genotyped based on nine highly polymorphic microsatellite markers. to reach this goal, different genetic distances based on infinite allele model (iam), stepwise mutation model (smm) and drawing phylogentic trees on un-weighted pair-group method using arithmetic averages (upgma) method w...