Editing Sequence alignment (section)

==Software==
{{Main|Sequence alignment software}}
A more complete list of available software categorized by algorithm and alignment type is available at [[sequence alignment software]], but common software tools used for general sequence alignment tasks include ClustalW2<ref>{{cite web|url=http://www.ebi.ac.uk/Tools/msa/clustalw2/|title=ClustalW2 < Multiple Sequence Alignment < EMBL-EBI|last=EMBL-EBI|website=www.EBI.ac.uk|access-date=12 June 2017}}</ref> and T-coffee<ref>[https://web.archive.org/web/20080918022531/http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi T-coffee]</ref> for alignment, and BLAST<ref>{{cite web|url=http://blast.ncbi.nlm.nih.gov/Blast.cgi|title=BLAST: Basic Local Alignment Search Tool|website=blast.ncbi.nlm.NIH.gov|access-date=12 June 2017}}</ref> and FASTA3x<ref>{{cite web|url=http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml|title=UVA FASTA Server|website=fasta.bioch.Virginia.edu|access-date=12 June 2017}}</ref> for database searching. Commercial tools such as [[DNASTAR|DNASTAR Lasergene]], [[Geneious]], and [[PatternHunter]] are also available.  Tools annotated as performing [http://edamontology.org/operation_0292 sequence alignment] are listed in the [https://bio.tools/?page=1&function=%22Sequence%20alignment%22&sort=score bio.tools] registry.

Alignment algorithms and software can be directly compared to one another using a standardized set of [[Benchmark (computing)|benchmark]] reference multiple sequence alignments known as BAliBASE.<ref name=thompson2>{{cite journal | journal=Bioinformatics | volume=15 | pages=87–8 | year=1999  |author1=Thompson JD |author2=Plewniak F |author3=Poch O | title=BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs | pmid=10068696 | doi = 10.1093/bioinformatics/15.1.87 | issue=1 | doi-access=free }}</ref> The data set consists of structural alignments, which can be considered a standard against which purely sequence-based methods are compared. The relative performance of many common alignment methods on frequently encountered alignment problems has been tabulated and selected results published online at BAliBASE.<ref>[https://web.archive.org/web/20121130084356/http://bips.u-strasbg.fr/fr/Products/Databases/BAliBASE/prog_scores.html BAliBASE]</ref><ref name=thompson3>{{cite journal | journal=Nucleic Acids Res | volume=27 | pages=2682–90 | year=1999  |author1=Thompson JD |author2=Plewniak F |author3=Poch O. | title=A comprehensive comparison of multiple sequence alignment programs | url= | pmid=10373585 | doi = 10.1093/nar/27.13.2682 | issue=13 | pmc=148477 }}</ref> A comprehensive list of BAliBASE scores for many (currently 12) different alignment tools can be computed within the protein workbench STRAP.<ref>{{cite web|url=http://3d-alignment.eu/|title=Multiple sequence alignment: Strap|website=3d-alignment.eu|access-date=12 June 2017}}</ref>