A nexus (phylogenetics) file reader and writer (.nex, .trees)
Project description
commonnexus
This package provides functionality to read and write the Nexus file format as specified in
Maddison, Swofford, and Maddison (1997). "NEXUS: An extensible file format for systematic information". Systematic Biology. 46 (4): 590–621. doi:10.1093/sysbio/46.4.590
Rather than trying to rip out relevant portions of a Nexus file as quickly as possible, the implementation
in commonnexus tries to do "the right thing" according to the specification, i.e. parse a file token by
token. Thus, we sacrifice speed for correctness and the ability to support weird edge cases like
Comments do not break tokens. Thus,
AssuMP[comment]TiONSis processed asASSUMPTIONS.
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