<!here>, While independently investigating the duplicate FASTA headers mentioned in relation to PR #68, I noticed a broader issue in the phylogeny subworkflow. Currently, all sample consensus FASTAs are combined and passed directly to MAFFT. This raises a concern for multi-contig reference genomes such as _P. falciparum_: simply adding sample IDs to the FASTA headers would prevent duplicate identifiers, but would not ensure that homologous contigs are aligned correctly. Could we clarify the intended scope of the phylogeny subworkflow? Is it intended to support whole-genome phylogenies for multi-contig references, or is the current implementation primarily designed for single-contig references? I'd like to understand the intended approach before suggesting any changes.