SeqMan Pro assembly can gather ESTs into organized groups that represent the same or similar genes or alleles, according to the match criteria you set. Since sequencing errors can be frequent in EST data, a significant challenge with EST assemblies is knowing whether a contig contains ESTs for a single allele, one or more alleles of a single gene, or multiple sequences corresponding to multiple homologs.
SeqMan Pro’s editing and post-assembly tools can be of assistance in differentiating these possibilities. Of particular value is identifying conflict split regions which searches for groups of conflicting nucleotides based on criteria that you specified under the Conflict Split parameters. By experimenting with these parameters, you should be able to split contigs from EST assemblies so that homologs are separated into individual genes or genes into individual alleles.