Proteins sequence selection criteria for Phylogenetic Tree

Question

[bushrajavedmalik]

Hi,

I am wondering if anyone can help me. I am new to Bioinformatics, doing background reading to understand the concepts.

I need to construct Phylogenetic tree of Tree nuts. I have total 32 plant species. I have downloaded sequences from UniProt, total number of sequence are 2890. Now the question is what type of sequences should be considered?

These sequences included full length sequence, fragments, sequence with signal peptides, encoding sequences (for PRC detection). Among 32 one plant species is the hybrid one.

I read somewhere I need to exclude the fragments, those sequences which contain signal peptides, encoding sequence. is it correct?

Another question, Clustal omega allowed only 2000 sequences at a time. Is there any other software which I can use?

Answer 1

[5heikki]

A good starting point would be to identify all the proteins that are present in all the 32 species as single copy genes. Then you would concatenate those so that you would have 32 very long sequences to align..