Table 1 Benchmarking of getphylo. A comparison of getphylo, autoMLST and GTDB-tk All programs were run on random sets of 10 and 100 high quality (< 20 contigs; N50 > 1 Mb) Streptomyces genomes from the NCBI database. The time taken for each run and the normalised sum of the Robinson-Foulds distances (NSUMRF) are shown (8 vCPUs, 32GiB RAM, maximum frequency of 3.5 GHz). Full data is provided in the Supplementary Information
From: getphylo: rapid and automatic generation of multi-locus phylogenetic trees
Method | Genomes | Time 10 loci, s | Time all loci,s (number of loci) | NSUMRF, 10 loci | NSUMRF, all loci |
|---|---|---|---|---|---|
getphylo (This study) | 10 | 19 ± 1 | 281 ± 27 (562 ± 51) | 0.13 | 0.09 |
100 | 164 ± 34 | 712 ± 59 (92 ± 8) | 0.25 | 0.20 | |
autoMLST (Alanjary et al.[2]) | 10 | 245 ± 23 | 759 ± 272 (325 ± 23) | 0.11 | 0.09 |
100 | 1816 ± 371 | 4430 ± 881 (157 ± 10) | 0.27 | 0.21 | |
GTDB-tk (Chaumeil et al.[3]) | 10 | N/A | 312 ± 84 | N/A | 0.11 |
100 | N/A | 2429 ± 10 | N/A | 0.23 |