[BioPython] what to use for working with fasta sequences and alignments?

[Jan Kosinski]

Hi,

I am quite new in BioPython and I am a little bit confused when trying 
to use BioPython for working with fasta sequences and alignments.

For instance, I can read and parse fasta files with Bio.Fasta, return 
records (as Fasta.record class), iterate and so on. But then I am going 
to Bio.Fasta.FastaAlign module which offers FastaAlignment (subclass of 
Alignment class) class. However, this class has very limited methods and 
get_all_seqs and get_seq_by_num return SeqRecord object instead of 
Fasta.record (why??) what makes it hard to use Bio.Fasta.FastaAlign 
(with SeqRecord) for alignments with Bio.Fasta (with Fasta.record) for 
sequences. Maybe I am wrong but Biopython seems to be full of 
incompatibilities. Or one should know which modules and classes should 
not be used?

Could you recommend me what should I use for my work with fasta 
sequences and alignments? Which BioPython modules and classes? Or should 
I use other packages like CoreBio?

Thank you in advance for any guidelines,
Janek Kosinski