Guys, I need help with phylogeny. I am very new to this field and currently trying to position a bacterial strain. I have selected four crucial loci for the genus, but I am encountering limitations in employing a multilocus approach. I attempted to use Paup/Mrmodelblocks - Mrbayes; however, even though the individual tree for each locus yields an acceptable topology (confirmed through marker sequences), concatenating the different genetic sequences results in a significant error in the tree's topology. I have tried various solutions to rectify this issue, but despite seeking assistance from experienced friends, I haven't been able to resolve it.

This led me to explore new approaches, considering a phylogeny based more on genomes using orthofinder. Initially, it worked well, but when I attempted to repeat the process, my PC couldn't support it, even though it is a robust computer. I'm using Linux, and every time I try to use orthofinder again, the system restarts. Consequently, I sought another approach, utilizing iqtree. I repeated the process using a multilocus strategy, but once again, I can create individual trees for each region, yet I struggle to obtain an acceptable topology when concatenating the regions to generate the tree for the four chosen regions.

The program does concatenate the sequences, but when I try to run the command to generate the tree with nucleotide substitution models, it produces an error due to the size of the concatenated sequences.

I am in need of tips and alternatives on how to address this issue. Although I successfully used the new cognac package in R, considering it's a recent approach, I need to validate my data. Please assist me with any possible alternatives. Thanks.