This is an almost completely true account of me using ARB today.
Apart from discovering the button that kills people in ARB, today was the first day that I thought about the absurdity of using 3 different alignment programs to get my work done:
- I use SeaView to align my sequences and to view already-aligned sequences.
- I use Clustal primarily for its “range information” function, to trim my sequences at my conserved trim targets.
- I use ARB to import the alignments and make phylogenetic trees.
Perhaps one day, there will be one aligner program that does everything I need it to. Do you hear me, you bioinformaticists out there??
2 thoughts on “ARB Comics!”
Of course we hear you. 🙂
Have a look at SINA, I think I wrote it exactly for what you’re trying to do. If you use the SILVA databases, you can use the online version. If you want to incorporate sequences into your own alignment, you need to download it and run it locally.
Say you’ve got new_sequences.fasta and mydatabase.arb. Then running “sina -i new_sequences.fasta -o mydatabase.arb –ptdb mydatabase.arb –overhang=remove” will add the aligned and trimmed sequences to your ARB file. Setting “–overhang=edge” will move the bases it can’t match up with your already aligned sequences to the outside of the alignment. Simple enough?
Drop me a line if you need help. I love the comic! 🙂
Thanks for the suggestion, Elmar! I will try out SINA on my next batch of sequences and see how it works for me.