Hello,
I'm new to the bioinformatics world and would like a feedback on which MSA tool to use.
I want to find a consensus sequence in about 18000 sequences (from marine biology samples) from several kinds of cyanobacterias.
I am currently using the msa.package in Rstudio which gives me the option between, clustlaW, clustalOmega and MUSCLE. I tried to run clustalW which is supposed to be better at handling large dataset but my problem is that it has already been running for 10h and still gives nothing. Do you have any idea why ?
Of note the clustalOmega did it in less than 20min.
Many thanks in advance
Not sure why it isn't working well (I assume it's not actually written in R code and is using a faster language 'under the hood'?)
You could use profiling to find out if there are bottlenecks, look at the 'profvis' package.
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