HGTs in teleost fishes

All_pairwise_files_synteny: Micro-syntenic scores computed between all genes belonging to the same orthogroup. One file for each species comparison.

Blast_pipeline : Files needed to run the BLAST procedure to detect HGTs

BRAKER_annotation_files : BRAKER results (GFF3) for annotated species

Further_analysis: Files needed to reproduce the detailed analysis of each putative HGTs (manual search of genes in close species or in alternative genome assemblies, alignment and ML trees with closest fish proteins + uniprot proteins, flanking regions and transposable elements analysis). One folder for each HGT. 

HGT_result_files: Files needed to reproduce the analysis presented in the manuscript 

Ks_pipeline: Files needed to run the Ks procedure (including alignment and Ks computations) 

Selection_analysis: FitMG94, aBSREL and RELAX result files

N5.tsv : Phylogenetic Hierarchical Orthogroups infered for the node N5 (= most recent common ancestor of all teleost fishes)

 Species_Tree : Species tree used in this study, computed using ASTRAL-III and dated using IQ-TREE2. This folder also contains all BUSCO gene trees used as input in ASTRAL-III.A first zipped folder with HOG alignments and phylogenetic trees can be found here, and need to be combined with those of the separate Zenodo directories (place the zipped folders Manuscript_Alignments_Trees_splitted.zip +  Manuscript_Alignments_Trees_splitted.z01 + Manuscript_Alignments_Trees_splitted.z02 +  Manuscript_Alignments_Trees_splitted.z03 + Manuscript_Alignments_Trees_splitted.z04 into the same location and run unzip Manuscript_Alignments_Trees_splitted.zip). [these files can be found here : 10.5281/zenodo.14012963 and 10.5281/zenodo.14012814]