A software package that significantly improves the completeness and accuracy of TCR/IG profiling from deep sequence data and includes procedures to identify novel alleles of gene segments. The alignment step in LymAnalyzer, which is based on a fast-tag-searching algorithm, results in rapid identification of VDJ gene segments, with significantly improved accuracy and completeness compared to existing tools applied to TCR data. In addition, LymAnalyzer can be applied to IG sequences, includes an integrated single nucleotide polymorphism (SNP) calling algorithm that identifies novel alleles of the VDJ gene segments and produces lineage mutation trees to represent the affinity maturation process of the IGs. On real and simulated data sets LymAnalyzer produces highly accurate and complete results. Although, to date we have applied it to TCR/IG data from human and mouse, it can be applied to data from any species for which an appropriate database of reference genes is available.