Lightweight program to merge alignment files, preserving partition information in Nexus CHARSET format. Assumes one gene per file (although this seems to be a reasonable extension to pursue). Does not assume the same taxon sampling across files; however, for taxa present across files, make sure names do not vary (or they will be interpreted as distinct). Currently takes in (vanilla) Nexus-formatted alignments as input, although fasta support is on the way. As always, line returns are assumed to be of unix flavour.
In a terminal prompt in the src directory, type:
make
Call as either:
./Meld2Nexus -c file1.NEX file2.NEX file3.NEX ... [-o outFileName]
or
./Meld2Nexus -f fileContainingNexusFileNames [-o outFileName]
where 'outFileName' is optional (default = "Merged.Nex").
For the second option, the executable and input files should be in the same directory. Otherwise, the file fileContainingNexusFileNames must use the path to the input files.
This is now implemented in the phyx program pxcat.