Making phylogenetic trees

Question

[dimitrischat]

Hello all,

Dont know if its the right place to ask. I have some repetitive human sequences and i wanna make a phylogenetic tree but in contrast with organisms like human/zebrafish/mouse or other. edit : Trying to find how to do this task. If anyone knew an online or local (linux) tool to do that, iwould appreciate it. Thanks in advance

[Joe]

So what exactly is the question?

[dimitrischat]

trying to find how to do this task. If anyone knew an online or local (linux) tool to do that.

[Joe]

We need to know much more information to give you an answer, including, but not limited to:

• How many sequences total?
• How long are the sequences (average/max)?
• Are they DNA or Protein?
• How divergent are they approximately?

[dimitrischat]

I have 26 repetitive human sequences, average 300 max 1000 bases. DNA. About your last point, they are similar repetitive sequences but in different chromosomes and different lenghts. I was asked to find a way to put these sequences in a phylogenetic tree alongside with organisms. But i cant find a way to do that.

[Joe]

How many sequences including the non human ones?

The short answer is:

• Download something like CLUSTAL/MUSCLE/T-Coffee/MEGA/MAFFT
• Get all of your sequences in a multifasta file in fasta format (with all of the representatives from the non-human species)
• Align (output an aligned fasta/phylip or some other alignment format)
• Use alignment to make a tree via IQ-Tree/iTOL/RAxML/FastTree. Whichever makes most sense.

Answer 1

[gb]

You could start here: https://www.ebi.ac.uk/Tools/msa/clustalo/

EDIT:

or here https://usegalaxy.org/

[dimitrischat]

thanks for the reply, but yea i already did a tree there with my 26 sequences, but i need to make a tree with these sequences + organisms and there is a limit (This tool can align up to 4000 sequences or a maximum file size of 4 MB). it would be ideal if i could maybe make a phylogenetic tree and visualize it in iTol

[gb]

ah, oke good to know. maybe galaxy?