A brief overview of the concepts, methods and computational tools used in phylogenetic tree construction and gene prediction

Abstract

The phylogenetic analysis encompasses several stages where the type of input data affects its specificity and usability. Because of the complexity and diversity of the analysis methods and tools, many users might be confused or misled. There are no easy guidelines to describe many of the molecular evolution approaches in simple and straightforward terms. Here, we have gathered information, algorithms, and methods to facilitate the selection of proper approaches based on the type of inputs and research questions. Additionally, principles for proper phylogenetic tree reconstruction, merits, and demerits of different methods were also evaluated. To facilitate understanding the diversity and capability of methods and tools and to abstract available information, several informative tables, and images were included that cover the contents of numerous literature in this field. This paper provides scientist from different field of research, with brief and straightforward methods and tools required for doing general molecular evolution analysis.