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Progressive, hierarchical, or tree methods generate a multiple sequence alignment by first aligning the most similar sequences and then adding successively less related sequences or groups to the alignment until the entire query set has been incorporated into the solution. The initial tree describing the sequence relatedness is based on pairwise comparisons that may include heuristic pairwise alignment methods similar to [[FASTA]]. Progressive alignment results are dependent on the choice of "most related" sequences and thus can be sensitive to inaccuracies in the initial pairwise alignments. Most progressive multiple sequence alignment methods additionally weight the sequences in the query set according to their relatedness, which reduces the likelihood of making a poor choice of initial sequences and thus improves alignment accuracy.
Many variations of the [[Clustal]] progressive implementation<ref name=higgins>{{cite journal | journal=Gene | volume=73 | issue=1 | pages=237–44 | year=1988 | author=[[Desmond G. Higgins|Higgins DG]], Sharp PM | title=CLUSTAL: a package for performing multiple sequence alignment on a microcomputer | pmid=3243435 | doi = 10.1016/0378-1119(88)90330-7 }}</ref><ref name=thompson>{{cite journal | journal=Nucleic Acids Res | volume=22 | pages=4673–80 | year=1994 | author1=Thompson JD| author2-link=Desmond G. Higgins |author2= Higgins DG|author3= Gibson TJ.|authorlink3=Toby Gibson | title=CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice | pmid=7984417 |pmc=308517 |url=http://nar.oxfordjournals.org/content/22/22/4673 |doi=10.1093/nar/22.22.4673 | issue=22 }}</ref><ref name=chenna>{{cite journal | journal=Nucleic Acids Res | volume=31 | pages=3497–500 | year=2003 |author1=Chenna R |author2=Sugawara H |author3=Koike T |author4=Lopez R |author5=Gibson TJ |authorlink5=Toby Gibson|author6=Higgins DG |authorlink6=Desmond G. Higgins|author7=Thompson JD. | title=Multiple sequence alignment with the Clustal series of programs | url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=12824352 | pmid=12824352 | doi = 10.1093/nar/gkg500 | issue=13 | pmc=168907 }}</ref> are used for multiple sequence alignment, phylogenetic tree construction, and as input for [[protein structure prediction]]. A slower but more accurate variant of the progressive method is known as [[T-Coffee]].<ref name=notredame>{{cite journal | journal=J Mol Biol | volume=302 | issue=1 | pages=205–17 | year=2000 | author1=Notredame C| author2-link=Desmond G. Higgins |author2= Higgins DG|author3= Heringa J. | title=T-Coffee: A novel method for fast and accurate multiple sequence alignment | pmid=10964570 | doi = 10.1006/jmbi.2000.4042 | url=https://semanticscholar.org/paper/701a93542d50c480699d7d0660f33875ae639dfd }}</ref>
===Iterative methods===
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