Progressive alignments are not guaranteed to be globally optimal. The primary problem is that when errors are made at any stage in growing the MSA, these errors are then propagated through to the final result. Performance is also particularly bad when all of the sequences in the set are rather distantly related. Most modern progressive methods modify their scoring function with a secondary weighting function that assigns scaling factors to individual members of the query set in a nonlinear fashion based on their phylogenetic distance from their nearest neighbors. This corrects for non-random selection of the sequences given to the alignment program.<ref name="mount"/>
Progressive alignment methods are efficient enough to implement on a large scale for many (100s to 1000s) sequences. Progressive alignment services are commonly available on publicly accessible web servers so users need not locally install the applications of interest. The mostA popular progressive alignment method has been the [[Clustal]] family,.<ref name="higgins1988">{{cite journal |author=[[Desmond G. Higgins|Higgins DG]], Sharp PM |year=1988 |title=CLUSTAL: a package for performing multiple sequence alignment on a microcomputer |journal=Gene |volume=73 |issue=1 |pages=237–244 |doi=10.1016/0378-1119(88)90330-7 |pmid=3243435}}</ref> especially the weighted variant ClustalW<ref name="thomson1994">{{cite journal | vauthors = Thompson JD, Higgins DG, Gibson TJ | title = CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice | journal = Nucleic Acids Res. | volume = 22 | issue = 22 | pages = 4673–80 | date = November 1994 | pmid = 7984417 | pmc = 308517 | doi = 10.1093/nar/22.22.4673 }}</ref> to which access is provided by a large number of web portals including [https://web.archive.org/web/20060705082556/http://align.genome.jp/ GenomeNet], [http://www.ebi.ac.uk/Tools/clustalw2/index.html EBI], and [http://www.ch.embnet.org/software/ClustalW.html EMBNet]. Different portals or implementations can vary in user interface and make different parameters accessible to the user. ClustalW is used extensively for phylogenetic tree construction, in spite of the author's explicit warnings that unedited alignments should not be used in such studies and as input for [[protein structure prediction]] by homology modeling. Current version of Clustal family is ClustalW2. EMBL-EBI announced that CLustalW2 will be expired in August 2015. They recommend Clustal Omega which performs based on seeded guide trees and HMM profile-profile techniques for protein alignments. TheyAn offeralternative different MSA toolstool for progressive DNA alignments. One of them is [[MAFFT]] (Multiple Alignment using Fast Fourier Transform).<ref name=EMBL-EBI>{{cite web|title=EMBL-EBI-ClustalW2-Multiple Sequence Alignment|url=http://www.ebi.ac.uk/Tools/msa/clustalw2/|website=CLUSTALW2}}</ref>
Another common progressive alignment method called [[T-Coffee]]<ref name="notredame2000">{{cite journal | vauthors = Notredame C, Higgins DG, Heringa J | title = T-Coffee: A novel method for fast and accurate multiple sequence alignment | journal = J. Mol. Biol. | volume = 302 | issue = 1 | pages = 205–17 | date = September 2000 | pmid = 10964570 | doi = 10.1006/jmbi.2000.4042 | s2cid = 10189971 }}</ref> is slower than Clustal and its derivatives but generally produces more accurate alignments for distantly related sequence sets. T-Coffee calculates pairwise alignments by combining the direct alignment of the pair with indirect alignments that aligns each sequence of the pair to a third sequence. It uses the output from Clustal as well as another local alignment program LALIGN, which finds multiple regions of local alignment between two sequences. The resulting alignment and phylogenetic tree are used as a guide to produce new and more accurate weighting factors.
Because progressive methods are heuristics that are not guaranteed to converge to a global optimum, alignment quality can be difficult to evaluate and their true biological significance can be obscure. A semi-progressive method that improves alignment quality and does not use a lossy heuristic while still running in [[polynomial time]] has been implemented in the program [http://faculty.cs.tamu.edu/shsze/psalign/ PSAlign].<ref name="sze2006">{{cite journal |vauthors=Sze SH, Lu Y, Yang Q |year=2006 |title=A polynomial time solvable formulation of multiple sequence alignment |journal=J Comput Biol |volume=13 |issue=2 |pages=309–319 |doi=10.1089/cmb.2006.13.309 |pmid=16597242}}</ref>
