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Clustering program based on NJ phylogeny

Does anyone have a recommendation for a clustering program that uses neighbor-joining phylogeny to cluster a dataset of protein sequences and output a representative from each cluster? I'm thinking of something that works like cdhit, but uses NJ instead of sequence identity for clustering.

Any suggestions?

clustering protein nj phylogeny
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updated by gbl1 gbl1 • written by kgbenn123 • kgbenn123

2 answers

Check http://evolution.genetics.washington.edu/phylip.html.

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written by leeandroid leeandroid

Phylip doesn't appear to have the function I'm looking for. I'm working with about 6000 seqs and want a program that can cluster through neighbor joining and output either a list of accessions that represent their respective clusters or some file format that allows me to extract them.

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written by kgbenn123 • kgbenn123

Even if late NJ (neighbourth joining) clustering is pretty easy to do on R function nj()

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written by gbl1 gbl1

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