Average run time and memory usage to align 100 query samples and to reconstruct ancestral sequence for the SARS2-100k dataset.

We estimated the run time and peak memory usage for the two preprocessing steps by TIPars. The first step of query sample alignment is necessary for all other alignment-based phylogenetic placement methods, e.g., UShER, EPA-ng, IQTREE-2 and APPLES-2. For the second step, once ancestral sequences have been reconstructed, they can be reused. Here we performed 10 runs of these two preprocessing steps: 1) aligning 100 SARS-CoV-2 samples to the reference hCoV-19/Wuhan/WIV04/2019|EPI_ISL_402124 using MAFFT (—addtotop); 2) inferring the ancestral sequences for the SARS2-100k dataset using PastML (ACCTRAN method) and present average timings. Tests were run on a server with 64 or 8 Intel Xeon Gold 6242 CPU cores. (XLSX)