What software has implemented algorithms for multiple sequence alignment of WGS fasta and GenBank format input?

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9.7 years ago

fashiondesignrussian ▴ 60

What software has implemented algorithms for modern multiple sequence alignment of WGS fasta and GenBank format input?

I could find only the SeqSphere.

I want to multialign 23 .gb reference files of MDR tuberculosis and 144 .gb and .fasta files from local MDR bacilli. Please advise what tools to use. Thanks

next-gen-sequencing wgs • 2.8k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by fashiondesignrussian ▴ 60

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It's not clear what you are trying to do. Regarding genbank format: simply convert everything to fasta format, and you can use any alignment software.

What kind of sequences are in those files and how many? I guess DNA, whole genome, single reads, contigs? Do you really want to do multiple-sequence alignment or align multiple sequences against a reference? What is your goal?

ADD REPLY • link 9.7 years ago by Michael 55k

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Whole genome sequences = WGS, want to run multiple-sequence alignment in various combinations to call SNPs thereafter and find differences in genomes, thanks, what software is best and fastest for WGS?

ADD REPLY • link 9.7 years ago by fashiondesignrussian ▴ 60

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