AFproject is a free service for objective performance comparison of alignment-free sequence comparison tools on different datasets.
This community developed web-service aims at simplyfing and standardizing the benchmarking of alignment-free tools. And for the users, the benchmarks provide a way to identify the most effective methods for the problem at hand.
AFproject reports performance assessment of alignment-free methods across 12 reference data sets, which are divied into 5 research applications.
|#||Research application||Reference data set||Sequence type||Read more|
|1||Regulatory Sequences||Cis-regulatory modules (CRM)||non-coding DNA|
|2||Protein Sequence Classification||Low sequence identity (<40%)||protein|
|High sequence indentiy (≥40%)||protein|
|3||Gene Tree Inference||SwissTree||protein|
|4||Genome-based Phylogeny||29 E.coli/Shigella strains||unassembled reads|
|29 E.coli/Shigella strains||full genomes|
|25 fish mitochondrial genomes||full genomes|
|14 plant species||unassembled reads|
|14 plant species||full genomes|
|5||Horizontal Gene Transfer||27 E.coil/Shigella strains||full genomes|
|8 Yersinia species||full genomes|
|33 simulated genomes||full artifical genomes|
AFproject provides performance reports of alignment-free methods for every reference data set. Click on a bar to see the report.
Provide us your own pairwise distances for given data set. After uploading your predictions, you will be able to compare the quality of your predictions against other alignment-free methods.
Developer uses the downloaded dataset as an input to his/her alignment-free program.
The server benchmarks the uploaded predictions and presents a report with the submitted method's performance and comparison to other available methods.
If you use the AFproject benchmarking service in your work, please consider citing:
Zielezinski et al. Benchmarking of alignment-free sequence comparison methods. Genome Biology, 2019, 20, p144. doi: 10.1186/s13059-019-1755-7