Revised Supplemental 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 revised Supplemental 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 methods<br>Supplementary Data S2. Alignment metrics for whole genome pairwise alignment<br>Supplementary Data S3. Alignment metrics for whole genome multiple alignment<br>Supplementary Data S4. List of genes in the two sorghum mini-genomes<br>Supplementary Data S5. List of genes in the Oryza sativa mini-genome<br>Supplementary Data S6. Mini-genome alignment rates across species<br>Supplementary Data S7. Multiple alignment summary metrics for 750 alignment parameters combinations. Alignments are based on syntentic sequences for mini-genome 1 (100-gene region on sorghum chr 3)<br>Supplementary Data S8. Multiple alignment summary metrics for 750 alignment parameters combinations. Alignments are based on syntentic sequences for mini-genome 2 (100-gene region on sorghum chr 1)<br>Supplementary Data S9. Whole genome pairwise alignment metrics of the 13 PACMAD species aligned to the maize reference using three parametrizations of LAST<br>Supplementary Data S10. Alignment performance of high-performing parameters compared to the default parameters and the cactus aligner<br>Supplementary Data S11. Genomic conservation scoring for multiple alignments generated with 750 alignment parameter combination compared to the default parameters<br>Supplementary Data S12. Custom LAST penalty matrices based on substitution rates calculated from Z. mays transposon alignments