Online pipeline for MSA and NJ tree generation bootstrap supported

Question

[lessismore]

Dear all,

can somebody recommend a simple and solid online pipeline for multiple sequence alignment (MSA) and tree generation (NJ) of about 1K protein sequences ? I've found https://www.ebi.ac.uk/Tools/msa/clustalo/ which seems to cover this goal but its not really clear to me how does it produce the nexus file for visualizing the tree + it shows only the branch length while i'm actually searching for some bootstrap analyses.

thanks in advance

Answer 1

[Andrzej Zielezinski]

Hi,

I highly recommend on-line service Phylogeny.fr. It performs:

• Multiple sequence alignment (Clustal / MUSCLE / T-Coffee / ProbCons)
• MSA curation (Gblock / remove positions with gaps)
• Tree construction with bootstrap (NJ / Parsimony / Maximum Likelihood / Bayes)
• Tree visualization