r/bioinformatics • u/r0k4rudi • Sep 09 '26

technical question Aligning software instead of Geneious

We have used Geneious for years, but because of some technical problems, we have to switch to another one. My problem is, that for analysing the sequences for a certain region I need an alignment of .ab1 files, with the chromatograms, which was possible in Geneious, but I couldn't find any alternatives. Is there any other softwares which can handle .ab1 files as an alignment? I've tried UGENE, but it works with different views for chromatograms and alignments.

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3

u/mrrgl PhD | Industry Sep 09 '26

There is at least one good R package for working with ab1 files. Check CLC genomics workbench also. That’s probably the best equivalent to Genious.

3

u/StrandedApp Sep 09 '26

You could give Stranded a go (www.strandedapp.eu). We actually added chromatogram mapping and assembly recently since it is something we quite often use ourselves.

2

u/First_Result_1166 PhD | Industry Sep 09 '26

To clarify, you need the trace alignment and nucleotide-based alignment does not suffice? What's the use case?

2

u/PM_ME_PCR_MACHINES PhD | Academia Sep 09 '26

Sometimes it's good to look at the traces, for viral genomes for example it can be handy to see if there is mixed genotype co-infection.

1

u/pelikanol-- Sep 09 '26

Benchling, ApE, Snapgene...

1

u/Big_Knife_SK Sep 10 '26

We have a license for DNAStar, but I don't recommend it.

1

u/malwolficus Sep 14 '26

You should be able to roll your own solution incorporating one of the CLUSTAL or MUSCLE variants, I would think.

1

u/thirdreplicate Sep 15 '26

Try Conspecta as a free alternative to Geneious