Questions and Clarifications Regarding Cognac Code

[Deblusantos]

Currently, I am engaged in research in the field of plant bacteriology, and during my investigations, I had the privilege of discovering and exploring Cognac, a tool developed by your team. I carefully read the associated article, and I must say that I am particularly impressed with the taxonomic approach that Cognac offers.

However, while attempting to implement some modifications in the code provided on GitHub, I encountered some challenges and would appreciate your guidance on specific points.

Firstly, I am interested in modifying the parameters related to the presence of marker genes. According to the understanding of the article and the potential flexibility of adjustable parameters in the tool, I aim to ensure the presence of marker genes in 100% of genomes, setting the "coreGeneThresh" parameter to 1. Similarly, I seek to ensure that genes are present in a single copy in 100% of genomes, establishing the "copyNumTresh" parameter as 0. Despite my efforts, I face difficulties incorporating these modifications and am having trouble obtaining the gene concatenation file.

Another issue I would like to address is related to phylogeny. In the article, I noticed the possibility of using the Maximum Likelihood (ML) methodology instead of Neighbor Joining (NJ) to infer the phylogenetic tree. Although I managed to obtain the NJ tree with the provided default code, I encountered challenges in implementing the necessary settings for the ML methodology. If possible, I would appreciate your guidance or suggestions on how to proceed in this regard.