Annotation of results from CD-HIT web server

Question

[pujaabhaskaranathan7079]

A lot of output files are generated as a result of cd-hit web server while checking for removal of redundant sequences. Which output file should I consider to visualize the results. How to open the output file.

[cpad0112]

Did you go through the documentation (https://github.com/weizhongli/cdhit/wiki)? It helps if you could post the output files you got and what you are looking for from the analysis. All output files are text files. Open it with text processors such as notepad++, st3.

Answer 1

[Mensur Dlakic]

It depends what you are trying to visualize. There are only two output files when you run it locally: a cluster (.clstr) file and a fasta file with non-redundant sequences. If you need to explore clusters, Joe has a parser (parseCDHIT.py) among his tools.