Matrix Concatenation: ConcatMatrices v1.2
A simple PERL script that concatenates two or more multiple sequence alignments (MSAs) in FASTA or NEXUS format. The number of sequences can vary between input files. The output consists of a single NEXUS file (ConcatMatrix.nex) that includes character sets for each of the original input files.
Only sequences with identical sequence identifiers will be concatenated, any sequences with unique identifiers will remain separate. The input files need to be in non-interleaved format (!) and are simply listed after the name of the script, either as filenames separated by a space or as/with wildcards enclosed in quotes. For example:
perl ConcatMatrices.pl data1.fasta data5.fasta data3.fasta
perl ConcatMatrices.pl ‘data*.fasta’