Hi!
I did cd-hit nucleotide. I selected the option “Sort cluster by size” and “sort FASTA by cluster size”. My doubt is does the representative sequence 1 correspond to cluster 0?
Hi @Ines_Leao
Yes, when computers list things out, the range always starts with a 0 for the first item. Any time you might see a first item count as a 1 instead, is was because the tool or program translated for you! 
I have a list of 6 things.
The position of the first item in my list is at 0.
The position of the last is at 5.
This is a nice explanation from engineers out in the wild. → https://cseducators.stackexchange.com/questions/5023/why-do-we-count-starting-from-zero
I also put a very simple example from the cd-hit tool test in this tiny shared history you can import and inspect to see how the two output files relate to each other.
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The first cluster is Cluster 0.
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The first sequence included in it, which is our representative sequence for Cluster 0, is itself counted at 0 since it the first item in a list of sequences.
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Other sequences that are clustered with that representative sequence will be listed after, starting with 1 (if there are any!), because they will always be the second or greater item in a cluster’s list of sequences.
Please give this a review and let us know if this is clear! You are welcome to screenshot or paste back the first few lines of your output and we can discuss the example lines closer.
Hi Jenna,
Thank you for your answer. However, the representative sequence 1, that should corresponde to cluster 0, does not have the same sequence size as showed in cluster 0.
Hi @Ines_Leao
We you like to share your history back, so I can take a closer look and try to help more specifically with your use case? You can post the link back here.
We can help to confirm there isn’t some problem with the tool, or that specific version of the tool, plus explain how to match up the files if that is needed.
Thanks!