1. Call_update_viruses.pl (calls update_viruses.pl) to give text file of novel accessions in NCBI Genomes.
2. Manually edit new_viruses.txt to give list of new accessions on new lines (new_accs.txt).
3. Call_new_refs2mysql.pl (calls new_refs2mysql.pl) to partially update segments table.
4. download flat file of all viral genomes from genome page (viral1.genomic.gbff.gz).
5. get_new_taxonomy.pl to get taxonomy.txt. Edit this manually in Excel then use populate_viruses.pl to populate viruses table from it.
6. call_populate_proteins.pl (calls populate_proteins.pl) to put basic protein data in table proteins.
7. Put virus id into proteins using virusid2proteins.pl.
8. Put coordinates into proteins using get_coordinates.pl (not available from BioPerl Genbank search).
9. Build coordinates tables using return_coords.pl.
10. Correct phase in coordinates with correct_phase.pl.
11. Save text copy of ICTV hml file from their website http://www.ictvdb.rothamsted.ac.uk/ICTVdB/index.htm. Run insert_ICTVdb_links.pl.
12. call_update_proteins.pl (calls update_proteins.pl) to fill other columns of proteins table
13. Run classify_protein.pl to put functions into proteins table.
14. Run make_all_proteomes.pl to put proteomes into table segments.
15. Find duplicate entries using associate_refseq_acc.pl.
16. Get other complete geneome sequences using call_isolate2mysql_align.pl (calls isolate...).
17. Run call_isolate2mysql_align_update.pl (calls isolate...) to update genomealigns in case of novel matches (replaces old with new alignments)
18. Put reference genome into genomealigns when no matches using put_ref_in_genomealigns.pl.
19. Calculate sequence divergence for table genomealigns using check_genomealigns.pl.
20. Put in biological details for table isolates using call_isolate2mysql.pl (calls isolate..).
21. Run output_aligns.pl to place all trees in directory new_trees.
22. Run trees2mysql to put trees into segments table.

NOTES
1. Duplicated new entry in NCBI Genomes for West Nile Virus (NC_009942, previously had NC_001563). Not included Mopeia Lassa reassortant 29 virus
2. Have not populated the overlap column in table coordinates.
3. No automated way of putting in viral abbreviations (texts from year 2000 only).
4. Made optional modification of call_isolate2mysql_align_update.pl to redo alignments if > 50 taxa in tree (problem with TGF). 
5. remove_bad_accs.pl is a modification of call_isolate2mysql_align_update.pl to redo alignments if divergence >=0.4 and/or alignment >1.5 length of feq seq. Need to ncorporate into main script.
6. Have not updated table isolates after final modifications.
