This link contains the entire dataset of our comparative genome analysis of 128 Phytophthora isolates. It contains various types of files with different extensions such as: - 1. *.fna files are the draft genome fasta sequence files. 2. *.faa files denote predicted protein files of the corresponding genome sequence. 3. *.ffn files contain the coding sequences (CDS). 4. *.gff3/gff files are the genomic feature format files. 5. *-eggnog.emapper.annotations files contain eggnog annotations of the genomes. 6. *.annot files contain annotations of genes located in extremely sparse regions of the genomes. 7. *.ssr files are the GMATA software predicted SSR files containing information regarding microsatellites. 8. *.ssr.sat2 files are also GMATA software output files storing statistics of predicted Simple Sequence Repeats (SSRs) in the genomes. 9. *_FIR are all combined FIR files. 10. *_rxlrFIR are RxLR FIR files. 11. *_crnFIR are CRN FIR files. 12. *_wylFIR are WYL FIR files. 13. *_buscoFIR are BUSCO FIR files. 14. *_RXLR_annotated are the predicted RxLR sequences for each genome. 15. *_rxlr.gff are gff files corresponding to predicted RxLRs. 16. PROTHINT.faa contains a proteome of 56 Phytophthora genomes.