[BiO BB] GCG gap program and emboss

[Peter Rice]

Hongyu Zhang wrote:
> Dear all,
> 
> I am wondering which program in the EMBOSS package is closest to the GCG gap program? and how similar is their performance in terms of sequence alignment and score?

Two EMBOSS programs have the same function (global alignment of nucleotide or 
protein sequences).

needle is a straight implementation of the Needleman Wunsch alignment algorithm

An alternative is stretcher, which is a port of the global alignment code in the 
FASTA package and can handle longer sequences by using a more memory-efficient 
order of processing.

The score is fixed by the algorithm so you should get the same results.

regards,

Peter Rice