When the user selects a new subprogram or click on an option field, a brief help related to this program or option is displayed on the top of the interface ( red arrows). It automatically generates the corresponding command line ( bottom left). The graphical user interface of MACSE v2 ( left) allows to select the desired subprogram, to browse the file system for choosing input FASTA files, and to set parameter values. Altogether, the subprograms implemented in the new MACSE v2 release compose a powerful toolkit now easily accessible through a graphical user interface ( fig. 1). Here we present a major update of MACSE with an improved version enriched by a series of subprograms aimed at facilitating the production and handling of multiple alignments of protein-coding sequences. 2013), and phylogenomic pipelines ( Bragg et al. 2012), metabarcoding analyses ( Leray et al. 2015), genome-wide analyses of selection ( Assis et al. Since its first release in 2011, MACSE has been used in multiple contexts including comparative transcriptomic studies ( Lan and Pritchard 2016), pseudogene evolution ( Delsuc et al. This allows one to produce nucleotide alignments that preserve the underlying codon structure while benefiting from the higher similarity of amino acid sequences. Its key feature is to align DNA sequences at the nucleotide level, but with the possibility to include gap lengths that are not a multiple of three bases, that is, generating frameshifts, while scoring the resulting nucleotide alignments based on their amino acid translation. Multiple Alignment of Coding Sequences (MACSE) was the first automatic solution developed to align multiple protein-coding nucleotide sequences based on their amino acid translation while allowing for the occurrence of frameshifts ( Ranwez et al. Multiple sequence alignment, molecular evolution, phylogenomics, pseudogenes, metabarcoding Brief Communication
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. Archives
January 2023
Categories |