Applied aspects of methods to infer phylogenetic relationships amongst fungi

There is a need to document the methodologies used for molecular phylogenetic analyses since the current fungal identification, classification and phylogeny are necessarily applied with DNA molecular sequence data. Hence this manuscript is mainly aimed to provide a basic reference or guideline for the mycologists venturing into the field of phylogenetic studies and to avoid unnecessary repetitions in related publications. This is not at all to elaborate the theoretical background but is intended as a compact guide of some useful software references and coding for the most commonly used phylogenetic methods applied in mycological research. This reference manuscript is originally conceived for usage with a set of programs necessary for inference of phylogenetic analyses in fungal research (taxonomy and phylogeny). For this purpose, principles, introductory texts and formulas have been omitted. Meanwhile, necessary steps from DNA extraction to DNA sequencing, sequences quality check, data alignment and general steps of phylogenetic tree reconstructions have been included.