Question: MSA alignment library for Java
gravatar for Bioaln
5.2 years ago by
Bioaln340 wrote:
Hello. I've come across an alignment project, which requires me to 'implement simple MSA' in Java. I know there are many great tools out there, but as I am to implement my software I need a hint on how to align multiple fasta sequences and write that to an outfile for example. I can use any library or implement algorithm from the scratch. Workload is not going to be very intensive, so a basic algorithm might work. Are there any libraries meant to do that? If not, where can i find sources on how to implement my own msa? Thanks for help.
alignment java sequence • 2.1k views
ADD COMMENTlink modified 5.2 years ago by vassialk200 • written 5.2 years ago by Bioaln340
gravatar for vassialk
5.2 years ago by
vassialk200 wrote:

If I correctly understand, look for Biojava or you can call BWA, Bowtie, BBMap, NextGene or use Ugene. Perhaps using Python or Ruby can be more laconic than Java.

ADD COMMENTlink written 5.2 years ago by vassialk200

Thanks for reply. I just discovered some of there options include Java API, which will probably solve my problem. In the end I am aiming to have an jar without calling other software. Therefore calling other programs is not an option. Thanks

ADD REPLYlink written 5.2 years ago by Bioaln340
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