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// $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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