/usr/include/libphylo/phylipFormat.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: phylipFormat.h 1812 2007-03-01 09:29:12Z adist $
#ifndef ___PHYLIP_FORMAT
#define ___PHYLIP_FORMAT
#include "definitions.h"
#include "sequenceContainer.h"
class phylipFormat {
public:
static sequenceContainer read(istream &infile, const alphabet* alph);
static void write(ostream &out, const sequenceContainer& sd,
const int numOfPositionInLine = 50,
const int spaceEvery = 10);
//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 PHYLIP FORMAT (interleaved):
6 128
Langur KIFERCELAR TLKKLGLDGY KGVSLANWVC LAKWESGYNT EATNYNPGDE
Baboon KIFERCELAR TLKRLGLDGY RGISLANWVC LAKWESDYNT QATNYNPGDQ
Human KVFERCELAR TLKRLGMDGY RGISLANWMC LAKWESGYNT RATNYNAGDR
Rat KTYERCEFAR TLKRNGMSGY YGVSLADWVC LAQHESNYNT QARNYDPGDQ
Cow KVFERCELAR TLKKLGLDGY KGVSLANWLC LTKWESSYNT KATNYNPSSE
Horse KVFSKCELAH KLKAQEMDGF GGYSLANWVC MAEYESNFNT RAFNGKNANG
STDYGIFQIN SRYWCNNGKP GAVDACHISC SALLQNNIAD AVACAKRVVS
STDYGIFQIN SHYWCNDGKP GAVNACHISC NALLQDNITD AVACAKRVVS
STDYGIFQIN SRYWCNDGKP GAVNACHLSC SALLQDNIAD AVACAKRVVR
STDYGIFQIN SRYWCNDGKP RAKNACGIPC SALLQDDITQ AIQCAKRVVR
STDYGIFQIN SKWWCNDGKP NAVDGCHVSC SELMENDIAK AVACAKKIVS
SSDYGLFQLN NKWWCKDNKR SSSNACNIMC SKLLDENIDD DISCAKRVVR
DQGIRAWVAW RNHCQNKDVS QYVKGCGV
DQGIRAWVAW RNHCQNRDVS QYVQGCGV
DQGIRAWVAW RNRCQNRDVR QYVQGCGV
DQGIRAWVAW QRHCKNRDLS GYIRNCGV
EQGITAWVAW KSHCRDHDVS SYVEGCTL
DKGMSAWKAW VKHCKDKDLS EYLASCNL
*/
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