Nexus
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Nexus file format is widely used in Bioinformatics. Several popular phylogenetic programs such as Paup*, MrBayes,Mesquite, and MacClade use this format. Command inside square brackets [ and ] are ignored (comment). Each block starts with BEGIN block_name; and finishes with END; An example for a simple DNA alignment would be:
#NEXUS
Begin data;
Dimensions ntax=4 nchar=15;
Format datatype=dna symbols="ACTG" missing=? gap=-;
Matrix
Species1 atgctagctagctcg
Species2 atgcta??tag-tag
Species3 atgttagctag-tgg
Species4 atgttagctag-tag
;
End;
(wikipedia)
