ictv-taxdump v39.2 for ICTV_Master_Species_List_2023_MSL39.v2

Generated with TaxonKit v0.16.0.

ictv-taxdump v38 for VMR_MSL38_v1

v38.0

update with taxonkit v0.14.0

ictv-taxdump v37.1 for VMR_19-250422_MSL37

Changes

• taxonkit create-taxdump stores TaxIds in int32 following BLAST and DIAMOND, rather than uint32 in previous versions.

ictv-taxdump v37 for VMR_19-250422_MSL37

Changes

• Include all ranks #1

• Better handle of taxa (mainly at subspecies rank) with the same names.
  For example, species Epseptimavirus ev329 and Salmonella virus 329 both have a "Virus name" Salmonella phage 3-29.

  $ cat ictv.taxonomy-with-subpsecies.tsv \
      | csvtk grep -t -f subspecies -p 'Salmonella phage 3-29' \
      | csvtk cut -t -f genus,species,subspecies \
      | csvtk pretty -t
  genus            species                subspecies
  --------------   --------------------   ---------------------
  Epseptimavirus   Epseptimavirus ev329   Salmonella phage 3-29
  Epseptimavirus   Salmonella virus 329   Salmonella phage 3-29
  

  They are assigned with different TaxIds and can be queried in taxid.map:

  $ grep 'Salmonella phage 3-29' ictv-taxdump-with-subpsecies/taxid.map 
  Salmonella phage 3-29   3010875164,3010875165
  
  $ grep 'Salmonella phage 3-29' ictv-taxdump-with-subspecies/taxid.map \
      | csvtk unfold -Ht -f 2 -s , \
      | taxonkit lineage --data-dir ictv-taxdump-with-subspecies/ -i 2 
  Salmonella phage 3-29   3010875164      Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Demerecviridae;Markadamsvirinae;Epseptimavirus;Epseptimavirus ev329;Salmonella phage 3-29
  Salmonella phage 3-29   3010875165      Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Demerecviridae;Markadamsvirinae;Epseptimavirus;Salmonella virus 329;Salmonella phage 3-29
  

ictv-taxdump v0.1.1 for VMR 18-191021 MSL36.xlsx

fixed missing class rank. shenwei356/taxonkit#57

ictv-taxdump v0.1.0 for VMR 18-191021 MSL36.xlsx

ictv-taxdump v0.1.0 for VMR 18-191021 MSL36.xlsx