FASconCAT-G, the product of a collaboration with Patrick Kück, offers a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignments for phylogenetic and population genetic analyses. The main functions include sequence renaming, file format conversion, sequence translation, consensus generation of predefined sequence blocks, and RY coding as well as site exclusions in nucleotide sequences and the generation of partitioned files for MrBayes and RAxML analyses. Process functions can be invoked in any combination and performed during a single process run. FASconCAT-G can also read in and handle different file formats (FASTA, CLUSTAL, and PHYLIP) in a single run.
For more details see kück&longo.2014.