/usr/include/libphylo/nexusFormat.h is in rate4site 3.0.0-2.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 | // $Id: nexusFormat.h 5158 2008-11-06 17:44:08Z itaymay $
#ifndef ___NEXUS_FORMAT
#define ___NEXUS_FORMAT
#include "sequenceContainer.h"
class nexusFormat{
public:
static sequenceContainer read(istream &infile, const alphabet* alph);
static void write(ostream &out, const sequenceContainer& sd);
//readUnAligned: the input sequences do not need to be aligned (not all sequences are the same length).
static sequenceContainer readUnAligned(istream &infile, const alphabet* alph);
};
#endif
/* EXAMPLE OF THE FORMAT:
#NEXUS
begin data;
dimensions ntax=6 nchar=128;
format datatype=Protein gap=-;
matrix
Horse KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGSSDYGLFQLNNKWWCKDNKRSSSNACNIMCSKLLDENIDDDISCAKRVVRDKGMSAWKAWVKHCKDKDLSEYLASCNL
Langur KIFERCELARTLKKLGLDGYKGVSLANWVCLAKWESGYNTEATNYNPGDESTDYGIFQINSRYWCNNGKPGAVDACHISCSALLQNNIADAVACAKRVVSDQGIRAWVAWRNHCQNKDVSQYVKGCGV
Human KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKPGAVNACHLSCSALLQDNIADAVACAKRVVRDQGIRAWVAWRNRCQNRDVRQYVQGCGV
Rat KTYERCEFARTLKRNGMSGYYGVSLADWVCLAQHESNYNTQARNYDPGDQSTDYGIFQINSRYWCNDGKPRAKNACGIPCSALLQDDITQAIQCAKRVVRDQGIRAWVAWQRHCKNRDLSGYIRNCGV
Cow KVFERCELARTLKKLGLDGYKGVSLANWLCLTKWESSYNTKATNYNPSSESTDYGIFQINSKWWCNDGKPNAVDGCHVSCSELMENDIAKAVACAKKIVSEQGITAWVAWKSHCRDHDVSSYVEGCTL
Baboon KIFERCELARTLKRLGLDGYRGISLANWVCLAKWESDYNTQATNYNPGDQSTDYGIFQINSHYWCNDGKPGAVNACHISCNALLQDNITDAVACAKRVVSDQGIRAWVAWRNHCQNRDVSQYVQGCGV
;
end;
NOTE!!!!
The seqeunces can also be ordered in an "interleaved" way:
Horse KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGS
Langur KIFERCELARTLKKLGLDGYKGVSLANWVCLAKWESGYNTEATNYNPGDES
Horse SDYGLFQLNNKWWCKDNKRSSSNACNIMCSKLLDENIDDDISCAKRVVRDKGMSAWKAWVKHCKDKDLSEYLASCNL
Langur TDYGIFQINSRYWCNNGKPGAVDACHISCSALLQNNIADAVACAKRVVSDQGIRAWVAWRNHCQNKDVSQYVKGCGV
*/
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