/usr/include/libphylo/molphyFormat.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: molphyFormat.h 962 2006-11-07 15:13:34Z privmane $
#ifndef ___MOLPHY_FORMAT
#define ___MOLPHY_FORMAT
#include "sequenceContainer.h"
class molphyFormat{
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 MOLPHY FORMAT:
6 128
Langur
KIFERCELARTLKKLGLDGYKGVSLANWVCLAKWESGYNTEATNYNPGDESTDYGIFQIN
SRYWCNNGKPGAVDACHISCSALLQNNIADAVACAKRVVSDQGIRAWVAWRNHCQNKDVS
QYVKGCGV
Baboon
KIFERCELARTLKRLGLDGYRGISLANWVCLAKWESDYNTQATNYNPGDQSTDYGIFQIN
SHYWCNDGKPGAVNACHISCNALLQDNITDAVACAKRVVSDQGIRAWVAWRNHCQNRDVS
QYVQGCGV
Human
KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQIN
SRYWCNDGKPGAVNACHLSCSALLQDNIADAVACAKRVVRDQGIRAWVAWRNRCQNRDVR
QYVQGCGV
Rat
KTYERCEFARTLKRNGMSGYYGVSLADWVCLAQHESNYNTQARNYDPGDQSTDYGIFQIN
SRYWCNDGKPRAKNACGIPCSALLQDDITQAIQCAKRVVRDQGIRAWVAWQRHCKNRDLS
GYIRNCGV
Cow
KVFERCELARTLKKLGLDGYKGVSLANWLCLTKWESSYNTKATNYNPSSESTDYGIFQIN
SKWWCNDGKPNAVDGCHVSCSELMENDIAKAVACAKKIVSEQGITAWVAWKSHCRDHDVS
SYVEGCTL
Horse
KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGSSDYGLFQLN
NKWWCKDNKRSSSNACNIMCSKLLDENIDDDISCAKRVVRDKGMSAWKAWVKHCKDKDLS
EYLASCNL
*/
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