Python中的生物信息学序列聚类

Question

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.

Answer 1

Two common used methods are:

• CH-hit, http://weizhongli-lab.org/cd-hit/
• Uclust (USEARCH, 32bit version is free) https://drive5.com/usearch/

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

Answer 2

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