New answers tagged software
I personally use more frequently Geneious for most of the basic every-day manipulations (my university bought a license), but I would recommend Ugene: it's free, open-source, cross-platform and supports batching and scenarios.
Geneious is probably the strongest standalone package, but real bionformaticians rarely deal with GUI driven programs.
I would strongly recommend benchling https://benchling.com This is an awesome web based tool for cloning, primer design, multiple sequence alignments and everything else you are used to doing with the other tools. It is very user friendly, and most importantly you can share designs with your collaborators. Also, the graphics are very beautiful. I recently ...
I would recommend Galaxy. https://usegalaxy.org/ The system does include primer design, sequence alignments and covers many common bioinformatics tasks.
For primer design you can use the Gene Designer: https://www.dna20.com/resources/genedesigner For sequence alignment you can use BLAST (from the NCBI, also downloadable as a standalone tool) Of course there are better options that might be more specific for your situation.
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