You can additionally build a graph of hypermutations for the sample using

java -jar MIGEC.jar CreateCdrHypermGraph final/S1.cdr3blast.txt net

which will generate files that allow fast network construction using Cytoscape’s network from table and import table routines for further data exploration.

Note that translated CDR3 sequences are obtained by simultaneously translating codons in two directions: from V and J segments to the middle of CDR3. If a frameshift is detected, the incomplete codon is added in lower case, with missing nucleotides marked as ?; stop codons are marked by *. CDR3 that contain either frameshift or stop codon are non-functional and are filtered by default. To include them into your output use -n option.

We also recommend to try out our new VDJtools software suite to perform post analysis of clonotype tables generated by MIGEC.