When sequencing a marker such as COI, sequences with different size of base pairs are obtained.
After aligning the sequences, it is observed that some sequences extend in the 3'-direction and in other cases in the 5'-direction.
What is the best way to carry out a phylogenetic analysis? Perform the analysis using the original size of the sequences, keeping as much information as possible and completing the information of the short sequences with "?".
Or cut the sequences is recommended and perform an analysis using as information, sequences of the same size.
Can you recommend an article that talks about this?
With your question it appears that you have a very little knowledge and understanding in the related topic, please get the basics of multiple sequence alignment and phylogeny. Also, read about Gblocks and trimAl to understand how trimming works in MSA and what are its shortfalls.
I would perform MAFFT (https://mafft.cbrc.jp/alignment/software/) for aligning (this software can will help in detecting the direction, and could change to reverse complementary if necessary). Then you could use GBlocks (http://molevol.cmima.csic.es/castresana/Gblocks_server.html) for a standarized trimming of sequences.
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