you need to use blstn in ncbi and retrieve the relevant sequences of your cloned sequences in diverse organisms and can make phylogenetic tree using mega7 software by using your and the retrieved sequences.

Hi Munirah Ramli

you can also download the Seqotron software (https://omictools.com/seqotron-tool) but it's done for MAC users.

fred

as Dr. Ujjal Kumar Nath has written the easiest way is to insert your DNA sequence in the blastn tool on the NCBI website paying attention to select Optimize forHighly similar sequences (megablast) to obtain only very similar sequences and then you can download the aligned sequences in .fasta, check if the sequences are properly aligned and use MEGA (https://www.megasoftware.net/) to construct a phylogenetic tree, probably a Neighbor Joining tree should be sufficient

if you want to use the amino acid sequence you can use blastx but I suggest you to use the DNA sequence since in this way you can also check the quality of the sequencing.

Domenico Benvenuto Thank you so much for your input. If I were to use blastx, how can I create a phylogenetic tree since my query sequence is a nucleotide sequence and the sequences given after blastx are amino acid sequences?

Frederic Lepretre Hello. Thanks so much for your input. Unfortunately I do not have access to a MAC. Would love to try this some day.

Ujjal Kumar Nath thank you so much for your help. I will try it out.

Munirah Ramli you can use MEGA as well but you have to select the proper options when you import the protein alignment, the process to construct the tree is almost identical but the results are less accurate