Recently, I am trying to built a phylogenetic tree using PhyloPhlAn. However, the output number of branches was not equal to the number of the inputs. The log file showed that parts of the genomes did not have enough markers in the genomes.
Is that OK to decrease the number of markers applied in the PhyloPhlAn.
Hello and thank you for using PhyloPhlAn.
Yes, you can lower the minimum number of markers (--min_num_markers param) each input genome has to have to be considered in the phylogenetic analysis. However, keep in mind that the genomes that map to only a few markers will have a very gappy alignment (because of the many missing markers). So you might want to increase the number of positions retained for each marker in the final MSA (--subsample param). You can find more details about these in the PhyloPhlAn wiki.
Many thanks,
Francesco