This project folder contains working data for the submission version of the Diatom HGT paper. Contributions are detailed here on the wiki page with a brief description (name, date, where to look). More detailed information (methodology, key results, take home messages) is provided in a **README** file for each directory **Contents** *All HGTs into Phaeodactylum genome*: (Richard Dorrell, 04/04/2020) details of single-gene trees, and internal BLAST hit top searches performed for 3067 genes from the version 3 annotation of the *Phaeodactylum tricornutum* genome with suspected histories of horizontal transfer, into or out of the ochrophytes, with both prokaryotic and eukaryotic partners. *Ochrophyte multigene tree*: (Richard Dorrell, 04/04/2020) details the construction and subsequent phylogenetic inspection of a concatenated 63-gene 213 taxa x 26613 aa alignment of all photosynthetic stramenopile lineages. *Localisation of HGTs*: (Richard Dorrell, 04/04/2020) details the *in silico* and GFP investigation of targeting biases in bacterial HGTs identified in ochrophyte species. *Coregulation of HGTs*: (Richard Dorrell, 05/04/2020) details Pearson correlation coefficient calculations of the coregulation of horizontally transferred gene of bacterial origin in the *Phaeodactylum tricornutum* genome using published microarray and RNAseq datasets. *Identification of chimeric sequences*: (Richard Dorrell, 05/04/2020) details the distribution of sequences of composite bacterial/ non-bacterial origin, as identified by BLASTp ranking analysis, in ochrophyte HGTs of bacterial origin identified through phylogenetic techniques. *ALE inference of bacterial HGTs*: (Benoît Perez-Lamarque, 08/04/2020) details the fasta alignment of the proteins clusters on which we performed ALE analyses, results of the ALE run (including randomizations), and results of the subsampling. *Supporting tables*: (Richard Dorrell, 13/04/2020) contains actualised supporting tables for the paper submission. *Paper figures*: (Richard Dorrell, 14/04/2020) contains actualised main text and supporting figures for the paper submission.