Change-O performs analyses of lymphocyte receptor sequences following alignment against the germline reference. It includes tools for standardizing the output of alignment software, clonal assignment, germline reconstruction, and basic database manipulation. Change-O was designed to be simple to use, but it does require some familiarity with commandline applications. To maximize flexibility, Change-O employs a simple tab-delimited database format with standardized column names, allowing easy use of Change-O output with external environments and interoperability with the Alakazam, SHazaM, and TIgGER R packages. A brief description of each tool is shown in the table below.

Tool Subcommand Description
AlignRecords   Multiple aligns sequences in a database
  across Aligns sequence columns within groups and across rows
  within Aligns sequence fields within rows
  block Aligns sequence groups across both columns and rows
AssignGenes igblast Runs IgBLAST on a fasta file
ConvertDb   Converts tab delimited database files
  airr Converts input to an AIRR TSV file
  changeo Converts input into a Change-O TSV file
  fasta Creates a fasta file from database records
  baseline Creates a special BASELINe formatted fasta file from a database
  genbank Creates fasta and feature table files for input to tbl2asn
CreateGermlines   Reconstructs germline sequences from alignment data
DefineClones   Assigns clones by V gene, J gene and junction distance
MakeDb   Creates standardized databases from germline alignment results
  imgt Parses IMGT/HighV-QUEST output
  igblast Parses IgBLAST output and adds IMGT-gapping to the V-segment
  ihmm Parses iHMMune-Align output
ParseDb   Parses annotations in tab delimited database files
  add Adds fields to the database
  delete Deletes specific records
  drop Deletes entire fields
  index Adds a numeric index field
  rename Renames fields
  select Selects specific records
  sort Sorts records by a field
  update Updates field and value pairs
  merge Merge files
  split Splits database files by field values