Blast is mainly used to quickly search large databases for sequences resembling a given query sequence. If you want to generate a multi-sequence alignment out of multiple related sequences, Clustal http://www.clustal.org is a good starting point. Which tools works best for you depends on whether you work with DNA or protein sequences, the level of similarity between the sequences and Your level of expertise: Web servers are easier to use, but local installations of the programs often allow you to better control parameters to tweak your alignment (e.g. gap insertion and gap elongation penalties). See this page for links to different alignment servers to try out which method. works best for you: https://www.ebi.ac.uk/Tools/msa/

Hi,

This is also a simple and fine web tool: http://tcoffee.crg.cat/

Hi Athena,

for my part I use tools from the UCSC web database in which you'll find a variant of best named BLAT (http://genome.ucsc.edu). it's useful for genomics alignments and it allows direct visualisation of results on a genome browser with lot of viewing options including custom tracks.

all the best

fred

Thank you. I will have a go at your recommendations, much appreciated!

Athena Andreosso

All the previous answers are good and solve your query.

However, I just wanted to mention one small point regarding what you said - "user-friendly."

In my experience, I have not come across with any aligner which was not user-friendly. But here, user-friendly refers to how a person sees it. Most software comes with user-manual and examples how to use it. If a user follows the manual, its user friendly. Also, the parameter selection can be a bit difficult and for me, it is not related to the user-friendliness of the software but to the experience of the user in alignment and understanding their target.

Conclusion-

If you want a software (for MSA) to be user-friendly in a real sense, try to understand the principle of MSA and go through the instructions in user-manual.

Few more fast and efficient aligners are:

MAFFT - https://mafft.cbrc.jp/alignment/server/

MUSCLE - https://www.ebi.ac.uk/Tools/msa/muscle/

FAMSA - https://www.nature.com/articles/srep33964