I have a sequence file (in fasta format) which has 12527 sequences and the length of each sequence is 61. I need to construct a phylogeny tree on this sequence. I am using a python package called "biopython" to perform the below steps:
- Use clustal omega command line tool to generate the alignment file.
- Read the alignment file generated and plot the phylogenetic tree.
However, clustal omega throws the following error:
HHalignWrapper:hhalign_wrapper.c:1419: problem in alignment (profile sizes: 1 + 1) (VS_bf95329ccdd7babf5bee3f5b2f5a2f50 + VS_b22382a3e858d9a132f3263009383220), forcing Viterbi hh-error-code=4 (mac-ram=8000) hhalign:hhalign.cpp:961: Problem Reading/Preparing profiles (len(q)=0/len(t)=0) HHalignWrapper:hhalign_wrapper.c:1447: problem in alignment, Viterbi did not work hh-error-code=4 (mac-ram=64000) hhalign:hhalign.cpp:961: Problem Reading/Preparing profiles (len(q)=0/len(t)=0) FATAL: could not perform alignment -- bailing out
When I perform clustalw2 on the same sequence, it works but takes too long. Can someone point out what exactly is the cause for the issue ?