ABSTRACT
Initially, phylogenetic trees were mostly used to provide a robust taxonomical classication based on the inference of phylogenetic relationships among species. Taxonomy is a formalized system of describing and naming objects. This topic remains current in modern mycology1,2 since the dual
3.1 Introduction: Why We Want to Make Phylogenetic Trees ..................................................... 15 3.1.1 Homology and Homoplasy ......................................................................................... 16 3.1.2 Paralogs, Orthologs, and Xenologs ............................................................................. 16 3.1.3 Reading Phylogenetic Trees ........................................................................................ 17
3.2 Major Steps of a Phylogenetic Analysis ................................................................................. 19 3.2.1 Input Format Issues..................................................................................................... 19 3.2.2 Dataset Selection ........................................................................................................20 3.2.3 Protein versus DNA Sequences ..................................................................................20 3.2.4 Sequence Alignment ...................................................................................................20 3.2.5 Positive Selection and Purifying Selection ................................................................. 21
3.3 Inferring Phylogeny ................................................................................................................22 3.3.1 Distance Methods .......................................................................................................23
