Welcome to AFproject

a joint effort to benchmark, improve and simplify alignment-free sequence analysis

Summary of service

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.

Service content

# 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
7 Yersinia species full genomes
33 simulated genomes full artifical genomes

Viewing benchmark results

Testing your own method

Download data set

Alignment-free method developer downloads from the AFproject server sequence set from one reasearch category.

E.g. fish mitochondiral genomes: See data set
Step 1
Calculate sequence distances

Developer uses the downloaded dataset as an input to his/her alignment-free program.

The output file should contain all-versus-all pairwise sequence distances in TSV/PHYLIP.
Step 2
Upload output

Developer uploads the output file to the server through form on the web site.

E.g. upload distances for mtDNA data set using the form
Step 3
Automatic Benchmark

The server benchmarks the uploaded predictions and presents a report with the submitted method's performance and comparison to other available methods.

By default, the report is private — visible only to the submitter — and the developer can choose if make the report publicly available or delete it.
Step 4