Construction of Phylogenetic Trees from Amino Acid Sequences using a Genetic Algorithm

نویسنده

  • Hideo Matsuda
چکیده

We have developed a novel algorithm to search for the maximum likelihood tree constructed from amino acid sequences. This algorithm is a variant of genetic algorithms which uses scores derived from the log-likelihood of trees computed by the maximum likelihood method. This algorithm is valuable since it may construct more likely tree from randomly generated trees by utilizing crossover and mutation operators. In a test of our algorithm on a data set of elongation factor-1 sequences, we found that the performance of our algorithm is comparable to that of other tree-construction methods (UPGMA, the neighbor-joining and the maximum parsimony methods; and the maximum likelihood method with di erent search algorithms).

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Phylogenetic and sequence analysis of the growth hormone gene of two sturgeons, Huso huso and Acipenser Gueldenstaedtii

In this study, the cDNA Growth Hormone (cGH) of the Belugasturgeon (Husohuso) and Russian sturgeon (Acipensergueldenstaedtii) were cloned and sequenced, and phylogenetic relationships were examined using nucleic acid and amino acid sequences. The nucleotide sequence of the Beluga GH has an open reading frame of 645 nucleotides encoding a protein 214 amino acid residues. The signal peptide cleav...

متن کامل

An Evolutionary Relationship Between Stearoyl-CoA Desaturase (SCD) Protein Sequences Involved in Fatty Acid Metabolism

Background: Stearoyl-CoA desaturase (SCD) is a key enzyme that converts saturated fatty acids (SFAs) to monounsaturated fatty acids (MUFAs) in fat biosynthesis. Despite being crucial for interpreting SCDs’ roles across species, the evolutionary relationship of SCD proteins across species has yet to be elucidated. This study aims to present this evolutionary relationship based on amino aci...

متن کامل

Protein phylogenetic inference using maximum likelihood with a genetic algorithm.

This paper presents a method to construct phylogenetic trees from amino acid sequences. Our method uses a maximum likelihood approach which gives a confidence score for each possible alternative tree. Based on this approach, we developed a genetic algorithm for exploring the best score tree: randomly generated alternative trees are rearranged so that their scores are improved by utilizing cross...

متن کامل

Fasciola gigantica of Ruminants: The phylogenetic analysis based on COX1 sequences

BACKGROUND: Fasciola species are parasitic trematode with world wide distribution that infects wild and domesticated herbivores, particularly ruminants. The aim of the present study was to investigate the intra species variations of F. gigantica, from goats and buffalos isolates in two common geographic climates of Iran. METHODS: Fasciola species were collected from goat, buffalo, sheep, and ca...

متن کامل

Quantitative Comparison of Tree Pairs Resulted from Gene and Protein Phylogenetic Trees for Sulfite Reductase Flavoprotein Alpha-Component and 5S rRNA and Taxonomic Trees in Selected Bacterial Species

Introduction: FAD is the cofactor of FAD-FR protein family. Sulfite reductase flavoprotein alpha-component is one of the main enzymes of this family. Based on applications of this enzyme in biotechnology and industry, it was chosen as the subject of evolutionary studies in 19 specific species. Method: Gene and protein sequences of sulfite reductase flavoprotein alpha-component, 5S rRNA sequence...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 1997