Hello, I am MSC student new to the field of bioinformatics and am currently analyzing ChIP-seq data for which peaks were called using the earlier version of MACS. A student in my lab recently re-ran peak calling on the data (histone marks and transcription factors) using MACS 2.0. We consistently obtain a smaller number of peaks with 2.0. Could someone tell me what the main difference between the two versions is and how that should affect the peaks called? Also, why is it that MACS 1.4 is still available for use? Thank you in advance!