http://www.trex.uqam.ca/index.php?action=hgt&project=trex

Boc, A., Philippe, H. and Makarenkov, V. (2010), Inferring and validating horizontal gene transfer events using bipartition dissimilarity, Systematic Biology, 59: 195-211

This tool is excellent!

Thanks Zhuofei Xu for your answer.

I have used this tool already (they have updated this tool and now seems excellent).

I have another question not directly reted with this topic:

If I am to detect HGT (suppose 12 species) using T-rex [where my intension is to find and remove xenologous gene sets and get pure orthologous gene set] and found 2 HGT -

Should I discard those gene sequence from my data ? Or  consider the whole gene as xonologous.

T-Rex do not explain this clearly.

Thank you again.

HGT is a not an easy question to answer. Even if some software says that a gene is horizontally transferred you can never be 100% certain. That being said, why dont you write your own script searching for HGT using simple tblastn. This paper (DOI: 10.1371/journal.pcbi.1004095) would give you some decent ideas.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2362129/

Raghunath chatterjee now have made several upgradation of his genomic Island concept. You may contact him personally to able to use his beta level newest modification of genomic Island. If needed, I can send you his contacts too.

Thank you everyone for your cordial response.

Dear Muhammad Khan

I can't access your link, it the site alive ?