A need to analyse specific sequences gathered from genbank in order to analyse primers matching/designing. I have used Sequencher (gene codes) in the past and I loved it. Yet prices are now prohibitive. Any suggestions?
Artemis can be used for primer alignment/design. Worst case you can use MUSCLE for alignment.
Wilsea Maria Figueiredo Wilsea, Here’s some ideas. But don’t know which is best for you. The first link is to ResearchGate member’s question. I'd start there and contact them with your question. Links as follows:
1)__ ResearchGate Question; "What is the best free download software for DNA sequence editing?"
https://www.researchgate.net/post/What_is_the_best_free_download_software_for_DNA_sequence_editing
2)__ Sequence Alignment Software
https://www.sequence-alignment.com/sequence-alignment-software.html#:~:text=Clustal%20%2D%20Perhaps%20the%20most%20commonly,command%20line%20interface%20(ClustalW)
3)__ SnapGene and Frequently Asked Questions
https://kb.mit.edu/confluence/pages/viewpage.action?pageId=154184583#:~:text=SnapGene%20automatically%20records%20the%20steps,richly%20annotated%20DNA%20sequence%20files
4)__ Golden Helix GenomeBrowse® tool
https://www.goldenhelix.com/products/GenomeBrowse/#:~:text=Genome%20Browse%20is%20designed%20to,free%20for%20academics%20and%20students
5)__ List of open-source bioinformatics software
https://en.wikipedia.org/wiki/List_of_open-source_bioinformatics_software
6)__ Free software for sequence alignments, designing constructs , translating nucleotide sequence to amino acid?
https://www.reddit.com/r/bioinformatics/comments/atjejb/free_software_for_sequence_alignments_designing/?rdt=34869
I found that you can go pretty far with the 'Sequence Manipulation Suite' : https://www.bioinformatics.org/sms2/ supplemented with NCBI BLAST tools and others. webPCR is also great: http://pydna.pythonanywhere.com/
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