Hello,
I trimmed and assembled (Reverse and Forward) my sequences using CLC Main Workbench software. The trimming I did aims to remove poor quality 3’ and 5’.
I’m going to perform multiple alignment, haplotype diversity and phylogenetic tree, using other software (DnaSP, Arlquin and MEGA).
Those softwares need uniform size of sequences (same length).
I have about 120 COI sequences of different sizes (640-750bp). The expected size was 710 bp.
Is there any software or method to trim sequences at same length: either one by one or both together? Which size do I need to choose for this trimming in my case?
You can use MEGA to trim sequences together at same length. DNA chromatograms should be used to decide the final length.
I always use Bioedit: align the sequences, move to the "Edit" mode and remove the extremes not matching with the rest of sequences. You will get a square block of sequence. Don't forget going back to the "select/slide" before going on with your work.
I recommend to use MEGA6 or new version 7. Bioedit is also good for trim the extra length of the sequences.
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