T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes
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Updated: Mar 9, 2026

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
Published on: March 22, 2016
Michail Tsimpidis1, Georgios Bachoumis1, Kalliopi Mimouli1
1Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece.
Background:
Many computational tools that detect recombination in viruses are not adapted for the ongoing genomic revolution. A computational tool is needed, that will rapidly scan hundreds/thousands of genomes or sequence fragments and detect candidate recombination events that may later be further analyzed with more sensitive and specialized methods.
Results:
T-RECs, a Windows based graphical tool, employs pairwise alignment of sliding windows and can perform (i) genotyping, (ii) clustering of new genomes, (iii) detect recent recombination events among different evolutionary lineages, (iv) manual inspection of detected recombination events by similarity plots and (v) annotation of genomic regions.
Conclusions:
T-RECs is very effective, as demonstrated by an analysis of 555 Norovirus complete genomes and 2500 sequence fragments, where a recombination hotspot was identified at the ORF1-ORF2 junction.
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