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Bioinformatics tools to detect horizontal gene transfer (HGT) in genomes: Revision

Horizontal gene transfer (HGT), the “non-sexual movement of genetic material between two organisms” , is relatively common in prokaryotes and single-celled eukaryotes, but a number of factors combine to make it far rarer in multicellular eukaryotes. In order for a eukaryotic species to gain a gene by HGT, foreign DNA must enter the host nucleus, integrate into the genome, and in more complex organisms it must enter the sequestered germline in order to be transmitted to offspring. Once there, it must not experience strong negative selection, despite potential for genetic incompatibility with the host genome and mismatch between the niche of the donor and the host. Over the longer term, foreign DNA may become “domesticated” in the recipient genome and provide novel function.

Following are the popular tool to detect HGT in genomes:

 

T-REX

3.22

HGT detection

download & compile

20525630

 

RANGER-DTL

2.0

HGT detection

download binary

22689773

 

PhyloNet

3.6.1

HGT detection

download binary

18662388

 

Jane

4.01

HGT detection

download binary (!license!)

20181081

 

TREE-PUZZLE

5.3.rc16

HGT detection

download & compile

11934758

 

CONSEL

0.20

HGT detection

download

11751242

 

DarkHorse

1.5 rev170

HGT detection

download & install

17274820

 

HGTector

0.2.1

HGT detection

git clone

25159222

 

EGID

1.0

HGT detection

download

22355228

 

GeneMarkS

4.30

HGT detection

download binary (!license!)

9461475