TFastA https://bip.weizmann.ac.il/education/materials/gcg/tfasta.html

"TFastA does a Pearson and Lipman search for similarity between a protein query sequence and any group of nucleotide sequences. TFastA translates the nucleotide sequences in all six reading frames before performing the comparison. It is designed to answer the question, "What implied protein sequences in a nucleotide sequence database are similar to my protein sequence?"" (part of GCG package)

"Tfasta translates the database in all six reading frames. If it encounters a stop codon it will ignore it and concatenate the sequences surrounding the stop codon. This makes sure that you do not loose any putative coding regions, but has the side effect that you may, but accident, pick up a sequence that doesn't exist."

https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml

"The source code for the FASTA programs is available from GitHub: www.github.com/wrpearson/fasta36 branch v36.6.8 GitHub will always have the latest version of the FASTA code and the GitHub code will often be more current than the releases at the other sites."

Thank you Dr. Annemarie Honegger for your information. These seem to be very nice softwares and I am learning how to run them.

I think you can predict open reading frames (ORFs) from your sequences and then blast your target gene to all ORFs from each strain and then align them using some basic software such as Mega

I usually upload my genomes to RAST https://rast.nmpdr.org/ where they are annotated and aligned. Then I can extract the protein sequences that I want from the entire batch.

Thank you Dr. Vo phuoc Tuan for your answer. Actually I have the reference sequence and I can blast this gene to each genome to find its homologue, then copy the amino acid sequence of each strain and perform the protein alignment of all strains in Mega X or Seaview or similar softwares. However, the steps of blasting and copying took me too much time considering the huge number of genomes (>200 genomes) and multiple target genes I wanted to search, that's why I was asking for some softwares that can automatic do this job. Do you have any good suggestion on this matter?

Thank you Dr. Tamara Salloum for your answer. I also used Rast or Patric to annotate my genomes and then Snapgene to view and search for a target gene. This manual task would be fine when we only search for the gene in several genomes, but if we have a huge number of genomes and several target sequences, this will become a laborious task. Please let me know if you have any solution for this matter.

If you can use nucleotide sequence, not protein. I recommend using this software, ABRICATE.

https://github.com/tseemann/abricate

Make your own database with reference sequences. This software will align your genomes into databases and export results into Excel files.