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.
I want to cut them at same length (like all sequences at 550bp) make all of them in equal size.
How can I do it in MEGA? I have all consensus in a FASTA file. Is it normal to cut the right end before alignment when file is imported in MEGA?
Thank you
you can cut directly in MEGA 6. I also doing the same thing like you (combining forward and reverse sequence) and cut to make it uniform in size.
It's better you align the F & R DNA sequences first and then you can go for trimming them. This way you can see the equal length sequences in the alignment and can easily avoid many errors during cut. you also can refer some video protocols in youtube and Abnova, to make it more handy.
Cheers!
Before cutting the sequences, blast against the nucleotide database to see the reference sequences and compare it have a optimum size range with good chromatogram quality.
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