You have several options and this is a good overview:

https://en.wikipedia.org/wiki/List_of_sequence_alignment_software

I've used DNAstar, but there are several free packages that can actually do the job very well (such as UGENE).

The choice will depend of what you need to do (for example, for medium-scale genotyping by Sanger sequencing, a package such as Mutation Surveyer can save you considerable time - but it is not a free package)...

Good luck with your experiments!

Its a basic bioinformatics analysis and you don't need any commercial/paid software for it. Nevertheless, Unipro Ugene (http://ugene.net/) is full functional and free software which can do majority of NGS analysis jobs. It has a youtube tutorial too for start. Another excellent software for sequence visualization and editing etc is Aliview (http://www.ormbunkar.se/aliview/). If you use them well, you won't require any other software for your analysis and further advanced analysis.

• For a simple alignment there is bio edit
• https://www.softpedia.com/get/Science-CAD/BioEdit.shtml
• https://www.youtube.com/watch?v=aPEKX1B0lHU
• Or alignment tools in GenBank:
• https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&LINK_LOC=align2seq

I've been also using BIoEdit. You can download it from here: http://www.mbio.ncsu.edu/BioEdit/bioedit.html

It is no longer maintaned, but the current version does a good job trimming and aligning sequences, as well as launching search from GenBank.

Hello !

What if you have hundreds of coupled F/R sequences, from a clone database ? Does it exist a way to not perform contig assembly one by one ?

You can you BioEdit