Pan-gene analysis ================= Files: MaizeGDB_B73_pangene_2020_11.tsv.gz - pan-genes across all B73 assembly versions MaizeGDB_maize_pangene_2020_08.tsv.gz - pan-genes across all genome assemblies hosted at MaizeGDB Format: One gene set per line. Note that some gene sets have multiple gene models from the same assembly. Methods: Gene model CDS transcripts for each genome were pairwise aligned to all other genomes using: blastn -perc_identity 95 -evalue 1e-10 -outfmt "6 std qlen slen qcovs". Syntenic orthologs of pairwise alignment outputs were found using DagChainer with parameters -D 1000000 -g 40000 -A 4. All DagChainer pairwise syntenic ortholog outputs were then concatenated and run through the program MCL with the parameters -I 2.0 -te 20 --abc -o