Welcome to HyLiTE

HyLiTE (Hybrid Lineage Transcriptome Explorer) analyzes high-throughput transcriptome data from allopolyploid species.

Allopolyploidy describes the formation of a new hybrid organism from the union of two or more different parents. Allopolyploid species carry multiple copies of each gene (homeologs), which often exhibit unusual expression patterns. Homeolog expression levels can technically be determined from next generation sequencing data (RNA-seq), but in practice, assigning reads to one homeolog over another is extremely challenging, particularly on a whole-genome scale. HyLiTE automates this process, and allows gene expression patterns to be explored even in very complex allopolyploid species.

The latest version of HyliTE can be downloaded here.

If you use this software, please cite:

W Duchemin, P-Y Dupont, MA Campbell, ARD Ganley and MP Cox. 2015. HyLiTE: Accurate and Flexible Analysis of Gene Expression in Hybrid and Allopolyploid Species. BMC Bioinformatics 16:8.

Content

• HyLiTE manual, including a tutorial

• Format of the protocol file

• HyLiTE output formats

• HyLiTE algorithm

• HyLiTE documentation, classes and code

• Parameters file

Indices and tables

• Index

• Module Index

• Search Page

HyLiTE was developed by Prof Murray P Cox, Dr Pierre-Yves Dupont and Wandrille Duchemin

Contents

© Copyright 2013-2020 Murray Cox, Wandrille Duchemin, Pierre-Yves Dupont. Created using Sphinx 3.1.1.