/usr/include/libphylo/phylipSequentialFormat.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 | // $Id: phylipFormat.h 962 2006-11-07 15:13:34Z privmane $
#ifndef ___PHYLIP_INTERLEAVED_FORMAT
#define ___PHYLIP_INTERLEAVED_FORMAT
#include "definitions.h"
#include "sequenceContainer.h"
class phylipSequentialFormat {
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 (sequential):
6 128
Langur KIFERCELAR TLKKLGLDGY KGVSLANWVC LAKWESGYNT EATNYNPGDE
STDYGIFQIN SRYWCNNGKP GAVDACHISC SALLQNNIAD AVACAKRVVS
DQGIRAWVAW RNHCQNKDVS QYVKGCGV
Baboon KIFERCELAR TLKRLGLDGY RGISLANWVC LAKWESDYNT QATNYNPGDQ
STDYGIFQIN SHYWCNDGKP GAVNACHISC NALLQDNITD AVACAKRVVS
DQGIRAWVAW RNHCQNRDVS QYVQGCGV
Human KVFERCELAR TLKRLGMDGY RGISLANWMC LAKWESGYNT RATNYNAGDR
STDYGIFQIN SRYWCNDGKP GAVNACHLSC SALLQDNIAD AVACAKRVVR
DQGIRAWVAW RNRCQNRDVR QYVQGCGV
*/
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