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Generate sequence alignment and heatmap for TF binding sites

Hi, I'm looking for programs to generate heatmaps from DNA sequences (TF binding sites) and clusterize them. I like this type of figure but it's from a Matlab library, and I haven't found equivalents in R or else. Any suggestions? Thanks a lot!

Figure

alignment chip-seq logo heatmap
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updated by Asaf Asaf • written by rioualen rioualen

1 answer

You've got good old WebLOGO. It doesn't produce the heatmap but honestly, I think it doesn't add any information.

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written by Asaf Asaf

Yeah I know it, but I'm not looking to produce the logo, I'm rather interested in how the sequences possibly cluster into subgroups, or if they're more like a continuum.

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written by rioualen rioualen

So you can represent the MSA as a matrix and you plain heatmap

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written by Asaf Asaf

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