Trex-online

Parallel HGT-Detection infers a scenario of horizontal gene transfers for the given
pair of species and gene trees using parallel computation (useful for large data sets).

Paste your species tree in the Newick format:

(Synechocystis:1.0000,(((Prochlorococus:1.0000,((Nitrobacter:1.0000,(Mn_oxidizing:1.0000,(Xanthobacter:1.0000,Rhodobacter_sphI:1.0000):1.0000):1.0000):1.0000,((Pseudomonas:1.0000,(Endosymbiont:1.0000,(Thiobacillus_denI:1.0000,(Alcaligenes_chr2:1.0000,(Alcaligenes_H16_p:1.0000,Alcaligenes_Chr1:1.0000):1.0000):1.0000):1.0000):1.0000):1.0000,(Hydrogenovibrio_L2:1.0000,(Chromatium_L:1.0000,(Thiobacillus_f19859:1.0000,Thiobacillus_fe1:1.0000):1.0000):1.0000):1.0000):1.0000):10.0000):1.0000,(Synechococcus:1.0000,Anabaena:1.0000):1.0000):1.0000,(Prochlorothrix:1.0000,Anacystis:1.0000):1.0000):1.0000,(Prochloron:1.0000,(Cyanophora:1.0000,((Cyanidium:1.0000,((Porphyridium:1.0000,(Ahnfeltia:1.0000,Anthithamnion:1.0000):1.0000):1.0000,(Cryptomonas:1.0000,(Ectocarpus:1.0000,(Olistodiscus:1.0000,Cylindrotheca:1.0000):1.0000):1.0000):1.0000):1.0000):1.0000,(((Chlamidomonas:1.0000,(Euglena:1.0000,Pyramimonas:1.0000):1.0000):1.0000,(Cholrella:1.0000,Bryopsis:1.0000):1.0000):1.0000,(Coleochaete:1.0000,(Marchantia:1.0000,(Pseudotsuga:1.0000,(Nicotiana:1.0000,Oryza:1.0000):1.0000):1.0000):1.0000):1.0000):1.0000):1.0000):1.0000):1.0000);

Species tree file Pasted

Paste your gene tree in the Newick format:

(((((Mn_oxidizing:1.3000,((Rhodobacter_sphI:0.9000,Xanthobacter:1.2000):0.7000,(Alcaligenes_chr2:0.3000,(Alcaligenes_Chr1:0.2000,Alcaligenes_H16_p:0.1000):0.1000):0.7000):0.8000):0.9000,(Cyanidium:1.0000,((Porphyridium:0.6000,(Ahnfeltia:0.4000,Anthithamnion:0.8000):0.6000):0.4000,(Cryptomonas:1.1000,(Ectocarpus:1.0000,(Olistodiscus:0.8000,Cylindrotheca:1.1000):0.4000):0.6000):0.6000):1.1000):0.9000):3.8000,((Prochlorococus:0.8000,Hydrogenovibrio_L2:0.5000):0.8000,(Chromatium_L:1.3000,(Pseudomonas:2.2000,(Thiobacillus_fe1:1.0000,(Nitrobacter:0.8000,(Endosymbiont:1.2000,(Thiobacillus_f19859:0.6000,Thiobacillus_denI:0.2000):0.3000):0.6000):0.6000):0.6000):0.8000):0.6000):1.2000):1.0000,(Synechococcus:0.7000,Anabaena:0.8000):0.6000):1.3000,(Prochlorothrix:0.6000,Anacystis:1.1000):0.5000,(Synechocystis:0.6000,(Prochloron:0.2000,(Cyanophora:0.8000,(((Chlamidomonas:0.6000,(Euglena:0.6000,Pyramimonas:0.5000):0.2000):0.2000,(Cholrella:0.3000,Bryopsis:0.5000):0.2000):0.5000,(Coleochaete:0.3000,(Marchantia:0.5000,(Pseudotsuga:0.2000,(Nicotiana:0.5000,Oryza:0.5000):0.3000):0.4000):0.3000):0.3000):0.7000):0.6000):0.7000):0.3000);

Gene tree file Pasted

Data sets : Matte-Taillez et al. (2002, gene rpl12e, 14 species),
Delwiche and Palmer (1996, gene rbcL, 40 species)

Select the root of the species tree
(if the root is not specified in the Newick string and the checkbox is not checked, the tree will be rooted by midpoint)

Select the root of the gene tree
(if the root is not specified in the Newick string and the checkbox is not checked, the tree will be rooted by midpoint)

Optimization criterion

Bipartition dissimilarity
Robinson and Foulds distance
Least-squares

Windows version of HGT-Detection
UNIX/Linux version of HGT-Detection

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