FASconCAT is designed to concatenate different nucleotide, amino acid and structure sequence fragments of same taxa to one supermatrix file in FASTA, PHYLIP or NEXUS format which can be used for phylogenetic purposes. Because of the fact that sequence concatenation is normally used to multiple sequence alignments, sequences must have equal length within each file. FASconCAT can handle input files in PHYLIP, CLUSTAL and FASTA format. There has to be no unique input format setting. FASconCAT can handle all different formats by one single run. FASconCAT extracts taxon specific associated gene- or structure sequences out of given input files and links them to one string. Missing taxon sequences in single files are replaced either by 'N', 'X' or by 'dots', dependent on their taxon associated data level (nucleotide, amino acid or "dot-bracket" structures).
Additionally to the supermatrix file (FASTA format) FASconCAT delivers a second file in .xls format including single range information of each sequence fragment and a check list of all concatenated sequences. The information file includes also additional reports about e.g. base composition of single and supermatrix files for nucleotide data and lists single loop- as well as stem pairing positions if structure sequences in dot bracket format are found. Concatenated structure sequence as well as loop and stem positions are also printed in a separate .txt file if extended information option is chosen. Under further options, FASconCAT can generate NEXUS files of concatenated sequences, with Mr.BAYES commands which can be directly executed by PAUP. FASconCAT was written on Linux and works on WindowsPCs, Macs and Linux running systems.