Contents of PanOryza pan-genes release v1.0 :

1. The Input fasta and gff folder contains the genomic DNA sequences and the annotation information of the genomes used for running GET_PANGENES pipeline. 

	- Nipponbare_gene_to_transcript_map.txt : tabular details of the pangene identifier and the corresponding gene ids from the 3 Nipponbare annotations (RAPDB, MSU and Gramene).

2. Os4530.POR.1 contains the pangene cluster sequences - genomic(gdna.fna) , cDNA(cDNA.fna), coding sequence(cds.fna), amino acids (cds.faa) and the output files of GET_PANGENES pipeline. 

	- POR.1.clusters_summary : Summarised tabular details of the pangene clusters , gene ids of the rice genome under that cluster, protein length etc. 

 
3. Pan_gene_matrix_transcripts.txt : Pan-gene matrix with re-ordered pangene identifier in 1st column and pan-gene cluster members in subsequent columns.

4. manuscript_data : Workspace files (.RData) to reproduce the manuscript analyses. The codes and other tables are available at GitHub. 

5. README.txt