Pangenome gene alignments of 41 Pseudorhizobium and Neorhizobium strains

All predicted protein sequence were extracted from the 571Rhizob genome dataset and clustered into homologous gene families (with possibly multiple copies per genome) using MMSeqs2 release 2 (commit e5d64b2) (Steinegger & Söding 2017). Protein sequences from each gene family were aligned using ClustalOmega (Sievers et al. 2011) and reverse-translated into coding sequence (CDS) alignments using PAL2NAL (Suyama et al. 2006).This resulted in the extensive Dataset presented in https://doi.org/10.6084/m9.figshare.8343473. Alignment file set and sequence content were then restricted to sequences occurring in the the 41NeoPseudo sub-dataset, resulting into 6,714 gene family alignments.