The NEXUS file format has a header with lines identifying the name of each of the sequences in the file, followed by lines that begin with the sequence name and some data. An example of part of an input file is:
#NEXUS
BEGIN DATA;
DIMENSIONS NTAX=17 NCHAR=428;
FORMAT DATATYPE=PROTEIN INTERLEAVE MISSING=-;
[Name: Chloroflex Len: 428 Check: 0]
[Name: Rcapsulatu Len: 428 Check: 0]
MATRIX
Chloroflex MSKEHVQTIATDDVSKNGHT PPTNASTPPYPFVAIVGQAE
Rcapsulatu ---------MTTAVARLQPS ASGAKTRPVFPFSAIVGQED
Chloroflex DQCRALEQQSGKTKKPAVIN IPVPVVDLPLGATEDRVCGT
Rcapsulatu DWATVLS-----TN---VIR KPTPVVDLPLGVSEDRVVGA
The MEGA conversion function looks for all the lines starting with the “[Name:” flag and takes the following word as a sequence name. The conversion function then scans through the data looking for all lines starting with each of the identified names and places them on the output. This appears as follows:
#mega
Title: infile.nexus
#Chloroflex
MSKEHVQTIATDDVSKNGHT PPTNASTPPYPFVAIVGQAE
DQCRALEQQSGKTKKPAVIN IPVPVVDLPLGATEDRVCGT
#Rcapsulatu
---------MTTAVARLQPS ASGAKTRPVFPFSAIVGQED
DWATVLS-----TN---VIR KPTPVVDLPLGVSEDRVVGA