How to trim sequences

Question

[PF]

Hello,

I'm a bit new to this stuff, but basically, I'm trying to construct a phylogeny based around the rbcL gene from several plant species. However, not all have it available in a short FASTA. For some species, only the whole genome is available, and so i extract the rbcL by taking a FASTA of the CDS region of rbcL. However, the issue is that it is significantly longer than the other rbcL Fastas, and I'm wondering how I could trim it to make them all the same length (if this is necessary, as I presume it is?).

Any help or guidance vids or links to similar threads would be appreciated.

Answer 1

[Mensur Dlakic]

Generally speaking, your don't trim individual sequences. Rather, you align them first and then trim the alignment. I will give you links to 2 programs that trim alignments.

• https://vicfero.github.io/trimal/
• https://research.pasteur.fr/en/software/bmge-block-mapping-and-gathering-with-entropy/