add clustalo to buildMSA

[jamesmkrieger]

Example:

In [1]: from prody import *

In [2]: filename = fetchPfamMSA('PF01094')
/home/jkrieger/software/miniconda/envs/prody-github/lib/python3.9/site-packages/urllib3/connectionpool.py:1099: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings
  warnings.warn(
@> Pfam MSA for PF01094 is written as PF01094_seed.sth.

In [3]: msa = parseMSA(filename)
@> 67 sequence(s) with 686 residues were parsed in 0.00s.

In [4]: msa_fixed = buildMSA(msa, method='clustalo')
@> 67 sequence(s) with 648 residues were parsed in 0.00s.

[jamesmkrieger]

clustalo actually doesn't seem to work very well, but clustalw can be installed from bioconda too

[karolamik13]

Works fine.

In [1]: from prody import *

In [2]: filename = fetchPfamMSA('PF01094')
/home/karolamik/anaconda3/envs/py39_tests/lib/python3.9/site-packages/urllib3/connectionpool.py:1099: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings
warnings.warn(
@> Pfam MSA for PF01094 is written as PF01094_seed.sth.

In [3]: msa = parseMSA(filename)
@> 67 sequence(s) with 686 residues were parsed in 0.00s.

In [4]: msa_fixed = buildMSA(msa, method='clustalo')
@> 67 sequence(s) with 648 residues were parsed in 0.00s.

[jamesmkrieger]

Have you tried clustalw too?