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pythoncluster-analysissequencebioinformatics
Hadij
Hadij

Reputation: 4600

bioinformatics sequence clustering in Python

I am trying to find a new method to cluster sequence data. I implemented my method and got an accuracy rate for it. Now I should compare it with available methods to see whether it works as I expected or not.

Is it possible to tell me what are the most famous methods in bioinformatics domain and what are the packages corresponded to those methods in Python? I am an engineer and have no idea about the most accurate methods in this field that I should compare my method to them.

Upvotes: 1

Views: 1476

Answers (2)

BioFrank
BioFrank

Reputation: 195

It also depends on the question for which tool you need(data reduction, otu clustering, making a tree, etc..). These days you see a shift in cluster tools that uses a more dynamic approach instead of a fixed similarity cutoff. Example:

  • DADA2
  • UNOISE
  • Seekdeep

Fixed clustering:

  • CD-HIT
  • uclust
  • vsearch

Upvotes: 2

candah
candah

Reputation: 124

Two common used methods are:

Both are command line tools and written in C++ (i think)

Upvotes: 2

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