/usr/include/libphylo/clustalFormat.h is in rate4site 3.0.0-5.
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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 42 43 44 45 46 | // $Id: clustalFormat.h 962 2006-11-07 15:13:34Z privmane $
#ifndef ___CLUSTAL_FORMAT
#define ___CLUSTAL_FORMAT
#include "sequenceContainer.h"
class clustalFormat{
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:
CLUSTAL V
Langur KIFERCELARTLKKLGLDGYKGVSLANWVCLAKWESGYNTEATNYNPGDESTDYGIFQIN
Baboon KIFERCELARTLKRLGLDGYRGISLANWVCLAKWESDYNTQATNYNPGDQSTDYGIFQIN
Human KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQIN
Rat KTYERCEFARTLKRNGMSGYYGVSLADWVCLAQHESNYNTQARNYDPGDQSTDYGIFQIN
Cow KVFERCELARTLKKLGLDGYKGVSLANWLCLTKWESSYNTKATNYNPSSESTDYGIFQIN
Horse KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGSSDYGLFQLN
Langur SRYWCNNGKPGAVDACHISCSALLQNNIADAVACAKRVVSDQGIRAWVAWRNHCQNKDVS
Baboon SHYWCNDGKPGAVNACHISCNALLQDNITDAVACAKRVVSDQGIRAWVAWRNHCQNRDVS
Human SRYWCNDGKPGAVNACHLSCSALLQDNIADAVACAKRVVRDQGIRAWVAWRNRCQNRDVR
Rat SRYWCNDGKPRAKNACGIPCSALLQDDITQAIQCAKRVVRDQGIRAWVAWQRHCKNRDLS
Cow SKWWCNDGKPNAVDGCHVSCSELMENDIAKAVACAKKIVSEQGITAWVAWKSHCRDHDVS
Horse NKWWCKDNKRSSSNACNIMCSKLLDENIDDDISCAKRVVRDKGMSAWKAWVKHCKDKDLS
Langur QYVKGCGV
Baboon QYVQGCGV
Human QYVQGCGV
Rat GYIRNCGV
Cow SYVEGCTL
Horse EYLASCNL
*/
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