ClassyFlu, BLAST and a phylogenetic approach have been applied to full gene sequences or fragments of the HA gene, from the NCBI Influenza Virus Resource and the GISAID EpiFlu influenza database with a release date between Jan. 2011 and Sep. 2012. This is a set of 1,033 sequences, 179 of them from GISAID. The results are provided in the following table: ClassyFlu vs. BLAST vs. PHYLO
These results are described in the article.


The algorithm was developed as part of the diploma thesis of Sandra Van der Auwera:
ClassyFlu-algorithm.pdf [3 MB]

Source code

The following archive contains all source code files to run the classification with locally. [1 MB]

The following archive contains all source code files to perform the HMM profile training with locally.
This training algorithm was used for the iterative, discriminative adjustment of the HMM parameters. [16 KB]

Additional example and README files are added to understand and run the program.

Training data

Accession numbers of NA training genes: allNtrain.lst