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est2genome -Align EST and genomic DNA sequences.
http://www.uk.embnet.org/Software/EMBOSS/Apps/est2genome.html

ESTatePage - Expressed Sequence Tag Analysis Tools Etc.
http://fe.hgmp.mrc.ac.uk/gslater/wwx/webwebx.cgi?ViewPage=ESTatePage

ESTs@EBI: JESAM - Clusters, Traces, Assemblies and Allocations.
http://corba.ebi.ac.uk/EST/jesam/

Expressed Sequence Tags - Research and Development.
http://industry.ebi.ac.uk/~muilu/EST/index.html

GeneNest: automated generation and visualization of gene indices.
http://www.dkfz.de/tbi/services/GeneNest/index

HarvESTer - EST clustering & assembly.
http://www.biomax.de/products/f_productsHarv.html

SEQtools - Program package for handling and analysis of nucleotide and protein sequences. In addition to many trivial functions, it includes advanced facilities for automated blast searching, sequence retrieval and design and layout of microarrays.
http://www.seqtools.dk/

Sputnik is an EST clustering, annotation and analysis pipeline that is being used to reconstruct partial plant transcriptomes. A variety of analyses are performed and data is cross-linked for expeditions into the world of comparative plant genomics.
http://mips.gsf.de/proj/sputnik/

The stackPACK data assembly system allows clustering and alignment of both ESTs and full-length sequences.
http://www.egenetics.com/?Section=Stackpack&Parent=products