How to interpret phylogenetic Dendrogram

Question

[nusrat.bot]

Hello Everybody,

For the first time, I have generated phylogenetic Dendrogram from about 4 family and 29 superfamily protein domain sequence from three species and assembled genomic data. My goal is to show how they are related or distantly related at the genomic level in terms of that specific protein domain sequence.

I have about 1000 protein motif sequence and I tried to draw a phylogenetic dendrogram from the family level and then divide the family in the superfamily.

My problem is now the dendrogram is so dense. Can anyone please tell me what will be the best way to show the differences that will I directly go the superfamily dendrogram preparation.:))) Sorry but I am not expert in this area

[Joe]

You can collapse nodes with most good tree drawing software, or do some clustering before you align to remove redudant sequences.

[nusrat.bot]

Daer jrj.healey, could you please tell me what kind of software I can use to do pre-clustering my protein sequence

[Joe]

CD-HIT is the most widely used tool. Others may know of alternatives.

[nusrat.bot]

Thank you very much:))

Answer 1

[Chirag Parsania]

Use this powerful online tool to create phylogenetic tree. You can select nodes from where you want to collapse tree. There are also various options available to make visualisation better. If you have ncbi ids, you can submit job to itol from phylot

[nusrat.bot]

Thank you very much, it will be very useful:))