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Seq-Gen-1.3.4/Seq-Gen-1.3.4/README

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+This package is the generic source-code version. This can be compiled
+and run on most UNIX/Linux/Mac OS X systems. It can also be compiled 
+for Windows. For Mac OS X a pre-compiled version is available from
+the website:
+
+http://tree.bio.ed.ac.uk/software/Seq-Gen/
+
+There is a manual in HTML format in the doc/ directory of this package.
+
+On most UNIX systems, to compile, type:
+
+cd source
+make
+
+A binary called 'seq-gen' will be created in the same directory as this
+README file.
+
+Any questions about Seq-Gen should be sent to:
+
+	Andrew Rambaut <[email protected]>

Seq-Gen-1.3.4/Seq-Gen-1.3.4/documentation/Using_Seq-Gen_with_PAUP

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+Seq-Gen by Andrew Rambaut and Nick Grassly
+
+Equivalent commands in PAUP and Seq-Gen:
+
+PAUP												Seq-Gen
+===================================================================================
+lset nst=2 variant=hky tratio=2.0;					-mhky -t2.0
+
+lset nst=6 rmat=(1.0 2.0 3.0 4.0 5.0);				-mrev -r1.0,2.0,3.0,4.0,5.0,1.0
+
+charpartition codon=1st:1-.\3,2nd:2-.\3,3rd:3-.\3;	-c0.3,0.2,2.5
+
+charpartition genes=RNA:1-300,CDS:301-1000;			-p3 (plus rates in treefile)

Seq-Gen-1.3.4/Seq-Gen-1.3.4/examples/example.tree

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+(((Taxon1:0.2,Taxon2:0.2):0.1,Taxon3:0.3):0.1,Taxon4:0.4);

Seq-Gen-1.3.4/Seq-Gen-1.3.4/examples/heterogeneity.tree

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+[300, 0.482364](((Taxon1:0.2,Taxon2:0.2):0.1,Taxon3:0.3):0.1,Taxon4:0.4);
+[400, 1.615264](((Taxon1:0.2,Taxon3:0.2):0.1,Taxon2:0.3):0.1,Taxon4:0.4);
+[300, 0.697283](((Taxon1:0.2,Taxon2:0.2):0.1,Taxon3:0.3):0.1,Taxon4:0.4);

Seq-Gen-1.3.4/Seq-Gen-1.3.4/examples/recombinant.tree

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+[400](((Taxon1:0.2,Taxon2:0.2):0.1,Taxon3:0.3):0.1,Taxon4:0.4);
+[600](((Taxon1:0.2,Taxon3:0.2):0.1,Taxon2:0.3):0.1,Taxon4:0.4);
+[300](((Taxon1:0.2,Taxon2:0.2):0.1,Taxon3:0.3):0.1,Taxon4:0.4);
+[400](((Taxon1:0.2,Taxon3:0.2):0.1,Taxon2:0.3):0.1,Taxon4:0.4);
+[300](((Taxon1:0.2,Taxon2:0.2):0.1,Taxon3:0.3):0.1,Taxon4:0.4);

Seq-Gen-1.3.4/Seq-Gen-1.3.4/examples/seqs+trees.phy

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+ 4 40
+Taxon1 ATCTTTGTAGTCATCGCCGTATTAGCATTCTTAGATCTAA 
+Taxon2 ATCCTAGTAGTCGCTTGCGCACTAGCCTTCCGAAATCTAG 
+Taxon3 ACTTCTGTGTTTACTGAGCTACTAGCTTCCCTAAATCTAG 
+Taxon4 ATTCCTATATTCGCTAATTTCTTAGCTTTCCTGAATCTGG  
+1
+(((Taxon1:0.2,Taxon2:0.2):0.1,Taxon3:0.3):0.1,Taxon4:0.4);

Seq-Gen-1.3.4/Seq-Gen-1.3.4/source/Makefile

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+CLINKER = cc 
+CLIBS = -lm
+
+RM = /bin/rm
+
+LIBS = $(CLIBS)
+
+CFLAGS = -O3
+
+OBJ = seq-gen.o global.o evolve.o model.o nucmodels.o aamodels.o eigen.o treefile.o progress.o gamma.o twister.o
+
+.SUFFIXES: .o .c .h
+
+.c.o:
+	$(CLINKER) $(CFLAGS) -c $*.c 
+
+dummy:	default
+
+clean:
+	$(RM) -f *~ *.o core
+
+default: all
+
+all: seq-gen
+
+seq-gen: $(OBJ)
+	$(CLINKER) $(CFLAGS) -o seq-gen $(OBJ) $(LIBS)
+
+%.o: %.c %.h
+	$(CLINKER) $(CFLAGS) -c $<

Seq-Gen-1.3.4/Seq-Gen-1.3.4/source/aamodels.h

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+/*  Header file for aamodels.c                             */
+
+/*  
+   Sequence Generator - seq-gen, version 1.3.4
+   Copyright (c)1996-2017, Andrew Rambaut & Nick Grassly
+   Institute of Evolutionary Biology, University of Edinburgh			
+   All rights reserved.                          
+
+   Redistribution and use in source and binary forms, with or without
+   modification, are permitted provided that the following conditions
+   are met:
+
+     1. Redistributions of source code must retain the above copyright
+        notice, this list of conditions and the following disclaimer.
+
+     2. Redistributions in binary form must reproduce the above copyright
+        notice, this list of conditions and the following disclaimer in the
+        documentation and/or other materials provided with the distribution.
+
+     3. The names of its contributors may not be used to endorse or promote 
+        products derived from this software without specific prior written 
+        permission.
+
+   THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+   "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+   LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+   A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+   CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+   EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+   PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+   PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+   LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+   NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+   SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+   Any feedback is very welcome.
+   http://tree.bio.ed.ac.uk/software/seqgen/
+   email: [email protected]
+*/
+
+#ifndef _AA_MODELS_H_
+#define _AA_MODELS_H_
+
+#include "evolve.h"
+
+#define NUM_AA 20
+#define SQNUM_AA 400
+#define CUNUM_AA 8000
+#define NUM_AA_REL_RATES 190
+
+enum { AA_NONE = -1, AA_JTT, AA_WAG, AA_DAYHOFF78, AA_BLOSUM62, AA_MTREV24, AA_CPREV45, AA_MTART, AA_LG, AA_GENERAL, numAAModels };
+
+extern char *aminoAcids;
+
+enum { ala, arg, asn, asp, cys, gln, glu, gly, his, ileu, leu, lys, met, phe, pro, ser, thr, trp, tyr, val};
+
+extern int aaFreqSet;
+
+extern double aaFreq[NUM_AA];
+extern double aaAddFreq[NUM_AA];
+extern double aaMatrix[MAX_RATE_CATS][SQNUM_AA];
+extern double aaVector[NUM_AA];
+
+extern double aaRelativeRate[NUM_AA_REL_RATES];
+
+void SetAAModel(int theAAModel);
+void SetAAMatrix(double *matrix, double len);
+void SetAAVector(double *vector, short state, double len);
+
+#endif /* _AA_MODELS_H_ */