Together with Vincent Ranwez and Nathalie Chantret, Frédéric participated in the writing of a book chapter on the practical use our multiple alignement program MACSE for protein-coding sequences. This chapter presents a practical overview and guidelines on the use of MACSE v2 and its integration into bioinformatic pipelines for handling large phylogenomic datasets. In particular we provide a detailed description of the OMM_MACSE pipeline that can be used as a singularity container to align and clean protein-coding sequence datasets. MACSE is used in the ConvergeAnt project to align large scale phylogenomic datasets to detect convergent molecular evolution in protein-coding sequences.
MACSE and associated pipelines are available from: http://bioweb.supagro.inra.fr/macse/index.php?menu=releases
MACSE v2 and OMM_MACSE are also available through dedicated web services at: http://mbb.univ-montp2.fr/MBB/
Ranwez V., Chantret N., Delsuc F. (2021). Aligning Protein-Coding Nucleotide Sequences with MACSE. In: Katoh K. (eds) Multiple Sequence Alignment. Methods in Molecular Biology, vol 2231. Humana, New York, NY. doi:10.1007/978-1-0716-1036-7_4