It depends upon whether you are sequencing a clone, a population of clones, DNA from a diploid organism, DNA from a polyploid organism, DNA from a viral swarn (such as HIV in a patient blood sample), etc.

In clones, there should be just one true sequence. In all of the others there can be two or more different sequences in the mix, and thus two or more bases at any given position. 

BioEdit is free software and can be useful for many projects, but it is not a modern day sequence assembler.  Today, there are many tools available for assembling genomes and dealing with "next generation" DNA sequencing data, that are far more advanced than BioEdit.  If you only have 5 or 10 forward and reverse sequences from Sanger sequencing, BioEdit may be enough.  But I would encourage you to learn to use more modern-day tools.

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003345

https://www.bioconductor.org/help/workflows/

https://omictools.com/genome-assembly-category

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137213/

Brian Thomas Foley 

Please give details how can I generate consensus sequence via BioEdit if I have Chromatogram files of both the forward and reverse sequence of ITS regions. I am confused as there are variations when I generate the conting sequence and compared to the contig sequences generated by experts for the same files.

If you could please give details regarding the formation of Consensus sequences via BioEdit. I have to either use fasta files or direct Chromatogram files in BioEdit software. Waiting for the complete guidance and details if you could please send sir.

Reagrds

Aashaq

BioEdit, Evgeny!

Dear Brian Thomas Foley 

Please give details how can I generate consensus sequence via BioEdit if I have Chromatogram files of both the forward and reverse sequence of ITS regions. I am confused as there are variations when I generate the conting sequence and compare that to the contig sequences generated by experts for the same files.

If you could please give details regarding the formation of Consensus sequences via BioEdit. Should I have to either use fasta files or direct Chromatogram files in BioEdit software. Waiting for the complete guidance and details if you could please send sir.

Reagrds

Aashaq

BioEdit can read trace/chromatogram files.  I am attaching the manual, I got from www.mbio.ncsu.edu/BioEdit/biodoc.pdf

Dear Brian Thomas Foley 

I saw your following reply on the same question I am asking. Can you please explain it in more detail. I followed your procedure you in recommend in the below reply, but not clear what to do with those which don't mach. Which bases are to be deleted and which to be kept. Please explain then how to get contig sequence. I will highly obliged if you could please explain it. 

It sounds like you already have the sequences of a PCR product, sequenced from the forward and reverse primers, in BioEdit. If this is true, you can easily convert the reverse sequence(s) to forward by selecting the reverse sequence(s) and then using the pull-down menu for Consequence Acid:Reverse Complement

This will "invert" your reverse sequence(s) so it (they) should now align with the forward sequence(s). You can use CLUSTAL which is built in to BioEdit for this, under the Accessory Application pull-down menu.

Once all of the sequences are aligned, you can easily highlight sites where not all of the sequences are identical using the pulldown menu for Alignment:Plot Identities to first sequence with a dot. Then you can decide which sites need to be checked in your original chromatograms to decide whether or not to edit a sequence.

BioEdit will also produce a consensus sequence with the pull-down menu item Alignment:Create Consensus Sequence, but it may be better to edit incorrect base calls first.