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PatrickKueck / FASconCAT-G

FASconCAT-G offers a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes. The main options 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. FASconCAT-G implemented process options 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.
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FASconCAT-G

FASconCAT-G is written on Linux and runs on Windows PCs, Mac OS and Linux operating systems. The program can be started directly via command line or through interactive menu options. Input files coming from Windows CRLF line feeds should be converted into Unix (LF) line feeds. This can be done in several editors (e.g., Bioedit or Notepad++). FASconCAT-G usually recognizes and converts these files but not in every instance. In order to run FASconCAT-G, open the terminal of your operating system and change directories to the folder where FASconCAT-G and your input files are located. Type the name of your FASconCAT-G version, followed either by a blank and your demand options in one row to start FASconCAT-G directly or just hit to open the FASconCAT-G menu. Notice that all input files have to be located in the FASconCAT-G home folder. To execute FASconCAT-G, a Perl interpreter must be installed on the current run system. Linux and Mac systems typically come with an interpreter pre-installed while Windows users will have to install a Perl interpreter (e.g., post). I recommend the ActivePerl interpreter.