ap_MSAColumnConservation reads a Multiple Sequence Alignment (MSA) in ClustalW or in FASTA format

and evaluates sequence conservation for every column

USAGE: ./ap_MSAColumnConservation cyped.CYP109.aln [M5R670_9BACI]

where cyped.CYP109.aln is the name of input MSA file (.aln or .fasta format). If the second optional argument (here: M5R670_9BACI) is given, program will attempt find the sequence annotated by this name. When such a sequence is found, additional column will be added to provide residue for every position in that sequence (gaps are also shown)



  • core::alignment::MSAColumnConservation