Supplementary Data: A multiple genome alignment workflow shows the impact of masking and parameter tuning on alignment of functional regions in plants

This dataset includes all Supplementary Data for the preprint titled "A multiple genome alignment workflow shows the impact of masking and parameter tuning on alignment of functional regions in plants". The data predominantly consists of Excel spreadsheets describing summary statistics and metrics for alignments of plant genomes. <br>Full descriptive names of all enclosed files are listed below.<br>Supplementary Data S1. Repeat masking results for grass genomes using three masking methodsSupplementary Data S2. Alignment metrics for whole genome pairwise alignmentSupplementary Data S3. Alignment metrics for whole genome multiple alignmentSupplementary Data S4. List of genes in the Sorghum mini-genomeSupplementary Data S5. List of genes in the Oryza sativa mini-genomeSupplementary Data S6. Mini-genome alignment rates across speciesSupplementary Data S7. Multiple alignment summary metrics for 750 alignment parameters combinationsSupplementary Data S8. Alignment performance of high-performing parameters compared to the default parameters and the cactus alignerSupplementary Data S9. Genomic conservation scoring for multiple alignments generated with 750 alignment parameter combination compared to the default parameters Supplementary Data S10. Custom LAST penalty matrices based on substitution rates calculated from Z. mays transposon alignments<br>