Horizontal gene transfer predictor tools

Horizontal gene transfer (or lateral gene transfer) is a type of recombination happening across species boundaries leaving an evident signature in the genome e.g. a change in nucleotide composition at the 3rd codon position. If the putative donor and recipient genomes are available, one can use bioinformatic tools to identify such areas and date the timing that such transfer occurred(Molecular clock analysis etc).
Some of the bioinformatics tools for this purpose are:
1)HybRIDS (Hybridisation, Recombination, Introgression and Dating Software). It is a bioinformatics tool designed to visualize the signal of recombination (and genetic introgression, horizontal gene transfer) in DNA sequence data present in large (multiple kb) contigs and whole genome sequence data of three or more individuals. It reports several summary statistics of these events, including breakpoint positions, number of SNPs, and it estimates the age of the recombination event. HybRIDS can also be applied to analyse smaller amplicons.
HybRIDS has a user-interface, and it is simple and relatively fast to run. The output of HybRIDS aims to direct the user to more computationally-intensive phylogenetic and population genetic analyses, e.g. to confirm the recombination events with multiple algorithms present in RDP3 (Martin et al. 2010), and/or date the divergence of the recombination blocks in a Bayesian framework, e.g. in BEAST (Drummond et al. 2012).
The analysis with HybRIDS consists of the following three-steps:
1. Load nucleotide data in FASTA format into the R environment using the user interface.
2. Analyse the sequence similarity of all possible sequence triplets with a sliding window approach.
3. HybRIDS then detects recombination blocks and calculates summary statistics for each recombination block (i.e. number of SNPs, breakpoint positions, length of recombination block, the probability that sequence similarity is caused by mutations rather than by recombination). HybRIDS also draws graphs of contigs illustrating the location of recombination blocks relative to base position, and it estimates the mean (5-95%CI) coalescence time of each recombination block, and it thereby dates each recombination event.
A beta version of HybRIDS is available from http://www.norwichresearchpark.com/ourresearch/researchgroups/elsa/software/hybrids.aspx
2.A webserver for this purpose can be accessed at: http://www.bioclues.org/horigene/predict.php
3.Another webserver combining three tools can be accessed at: http://bioinformatics.publichealth.uga.edu/SpeciesTreeAnalysis/