We published an updated and augmented version our multiple alignement program MACSE accounting for frameshifts in protein-coding sequences in Molecular Biology and Evolution (doi.org/10.1093/molbev/msy159). This new MACSE v2 version is enriched by a series of subprograms aimed at facilitating the production and handling of multiple alignments of protein-coding sequences. In order to make the program more accessible, we now provide a graphical user interface (GUI) facilitating access to the different subprograms. MACSE v2 is freely available from: https://bioweb.supagro.inra.fr/macse/. MACSE v2 and OMM_MACSE, a pipeline based on the MACSE v2 toolkit used to align the thousands of orthologous genes in the OrthoMAM database, are also available through dedicated web services at: http://mbb.univ-montp2.fr/MBB/. MACSE is used in the ConvergeAnt project to align pseudogene sequences to corresponding functional orthologous sequences.
Ranwez V., Douzery E.J.P., Cambon C., Chantret N. & Delsuc F. (2018). MACSE v2: toolkit for the alignment of coding sequences accounting for frameshifts and stop codons. Molecular Biology and Evolution 35: 2582-2584. doi:10.1093/molbev/msy159