We are using BIOPAC, but this one does not come as a freeware software. If you are looking for an open-source, freeware software, I would recommend HRVAS.
It is a MATLAB based HRV analysis tool with all the features Kubios have (time domain, frequency domain, time-frequency, Poincaré, nonlinear HRV analysis).
Please check out here: http://www.codesna.com/en/products/codesna_hrv/
CODESNA_HRV provides new and disruptive innovation in non-linear analysis (dynamic SNS and PNS activities, resting factor..) in top of standard analysis (FFT / RMSDD..).
Please let me know if you have any question on that!