Question: Getting Pairwise Sequence Alignment Score With Biopython
0
gravatar for Lakshmi
8.6 years ago by
Lakshmi0
Lakshmi0 wrote:

Hello,

I used the following code to run clustalw.I got an alignment file using this code. But I need to get pairwise sequence alignment score and also has to get distance matrix based on sequence identity.My aim is to do hierarchical clustering. How can I do these things with biopython.

import os
from Bio.Align.Applications import ClustalwCommandline
clustalw_exe = r"C:\Program Files\clustalw2\clustalw2.exe"
clustalw_cline = ClustalwCommandline(clustalw_exe, infile="C:\Users\pp\Desktop\myseqs.fasta") 
assert os.path.isfile(clustalw_exe), "Clustal W executable missing"
 stdout, stderr = clustalw_cline()
from Bio import AlignIO
align = AlignIO.read("C:\Users\pp\Desktop\myseqs.aln", "clustal")
print align
alignment clustalw biopython • 3.2k views
ADD COMMENTlink written 8.6 years ago by Lakshmi0

So you basically want to build a phylogenetic tree?

ADD REPLYlink written 8.6 years ago by Damian Kao15k

Thanks for your comment. Yes I would like to create a dendrogram.

ADD REPLYlink written 8.6 years ago by Lakshmi0
1
gravatar for Damian Kao
8.6 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

There are already plenty of software you can use to make a tree. You can try:

  • [?]EBI's ClustalW phylogeny tool[?]
  • [?]Mr Bayes[?]
  • [?]PHYLIP[?]
  • [?]A huge list of other phylogenetic tree generation software[?]

People usually tell me to us Mr Bayes.

ADD COMMENTlink written 8.6 years ago by Damian Kao15k

Thanks for your answer.I know about software. But I am trying to do this with Biopython.

ADD REPLYlink written 8.6 years ago by Lakshmi0
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