[med-svn] [seq-gen] 01/06: New upstream version 1.3.3+git4a8cc9d.ds
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Mon Sep 11 14:26:58 UTC 2017
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository seq-gen.
commit 8cfb759000dbe96d0d5f53b224a16a7c96221341
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Mon Sep 11 15:56:04 2017 +0200
New upstream version 1.3.3+git4a8cc9d.ds
---
source/aamodels.c | 88 ++++++++++++++++++++++++++++++++++++++++++++++++++----
source/aamodels.h | 12 ++++----
source/eigen.c | 12 ++++----
source/eigen.h | 10 +++----
source/evolve.c | 47 +++++++++++++++++++++++++----
source/evolve.h | 13 ++++----
source/gamma.c | 10 +++----
source/gamma.h | 10 +++----
source/global.c | 10 +++----
source/global.h | 10 +++----
source/model.c | 14 +++++----
source/model.h | 12 ++++----
source/nucmodels.c | 10 +++----
source/nucmodels.h | 10 +++----
source/progress.c | 10 +++----
source/progress.h | 10 +++----
source/seq-gen.c | 20 +++++++------
source/tree.h | 10 +++----
source/treefile.c | 17 ++++++-----
source/treefile.h | 10 +++----
source/twister.c | 12 ++++----
source/twister.h | 12 ++++----
22 files changed, 246 insertions(+), 123 deletions(-)
diff --git a/source/aamodels.c b/source/aamodels.c
index a924c44..3337ff4 100755
--- a/source/aamodels.c
+++ b/source/aamodels.c
@@ -1,7 +1,7 @@
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -33,8 +33,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#include <stdio.h>
@@ -122,6 +122,35 @@ static double wagFrequencies[NUM_AA] = {
0.0866, 0.0440, 0.0391, 0.0570, 0.0193, 0.0367, 0.0581, 0.0833, 0.0244, 0.0485, 0.0862, 0.0620, 0.0195, 0.0384, 0.0458, 0.0695, 0.0610, 0.0144, 0.0353, 0.0709
};
+/* LG model of amino acid evolution */
+/* Le, S. and Gascuel, O. (2008) An improved Amino Acid Replacement Matrix */
+/* Mol. Biol. Evol. 25(7):1307-1320. */
+static double lgRelativeRates[NUM_AA_REL_RATES] = {
+ 0.425093, 0.276818, 0.395144, 2.489084, 0.969894, 1.038545, 2.066040, 0.358858, 0.149830, 0.395337, 0.536518, 1.124035, 0.253701, 1.177651, 4.727182, 2.139501, 0.180717, 0.218959, 2.547870,
+ 0.751878, 0.123954, 0.534551, 2.807908, 0.363970, 0.390192, 2.426601, 0.126991, 0.301848, 6.326067, 0.484133, 0.052722, 0.332533, 0.858151, 0.578987, 0.593607, 0.314440, 0.170887,
+ 5.076149, 0.528768, 1.695752, 0.541712, 1.437645, 4.509238, 0.191503, 0.068427, 2.145078, 0.371004, 0.089525, 0.161787, 4.008358, 2.000679, 0.045376, 0.612025, 0.083688,
+ 0.062556, 0.523386, 5.243870, 0.844926, 0.927114, 0.010690, 0.015076, 0.282959, 0.025548, 0.017416, 0.394456, 1.240275, 0.425860, 0.029890, 0.135107, 0.037967,
+ 0.084808, 0.003499, 0.569265, 0.640543, 0.320627, 0.594007, 0.013266, 0.893680, 1.105251, 0.075382, 2.784478, 1.143480, 0.670128, 1.165532, 1.959291,
+ 4.128591, 0.267959, 4.813505, 0.072854, 0.582457, 3.234294, 1.672569, 0.035855, 0.624294, 1.223828, 1.080136, 0.236199, 0.257336, 0.210332,
+ 0.348847, 0.423881, 0.044265, 0.069673, 1.807177, 0.173735, 0.018811, 0.419409, 0.611973, 0.604545, 0.077852, 0.120037, 0.245034,
+ 0.311484, 0.008705, 0.044261, 0.296636, 0.139538, 0.089586, 0.196961, 1.739990, 0.129836, 0.268491, 0.054679, 0.076701,
+ 0.108882, 0.366317, 0.697264, 0.442472, 0.682139, 0.508851, 0.990012, 0.584262, 0.597054, 5.306834, 0.119013,
+ 4.145067, 0.159069, 4.273607, 1.112727, 0.078281, 0.064105, 1.033739, 0.111660, 0.232523, 10.649107,
+ 0.137500, 6.312358, 2.592692, 0.249060, 0.182287, 0.302936, 0.619632, 0.299648, 1.702745,
+ 0.656604, 0.023918, 0.390322, 0.748683, 1.136863, 0.049906, 0.131932, 0.185202,
+ 1.798853, 0.099849, 0.346960, 2.020366, 0.696175, 0.481306, 1.898718,
+ 0.094464, 0.361819, 0.165001, 2.457121, 7.803902, 0.654683,
+ 1.338132, 0.571468, 0.095131, 0.089613, 0.296501,
+ 6.472279, 0.248862, 0.400547, 0.098369,
+ 0.140825, 0.245841, 2.188158,
+ 3.151815, 0.189510,
+ 0.249313
+};
+
+static double lgFrequencies[NUM_AA] = {
+ 0.079066, 0.055941, 0.041977, 0.053052, 0.012937, 0.040767, 0.071586, 0.057337, 0.022355, 0.062157, 0.099081, 0.064600, 0.022951, 0.042302, 0.044040, 0.061197, 0.053287, 0.012066, 0.034155, 0.069147
+};
+
/* Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C. (1978)*/
/* A model of evolutionary change in proteins.*/
/* Dayhoff, M.O. (ed.) Atlas of Protein Sequence Structur., Vol5, Suppl. 3,*/
@@ -236,11 +265,50 @@ static double cprevFrequencies[NUM_AA] = {
0.076, 0.062, 0.041, 0.037, 0.009, 0.038, 0.049, 0.084, 0.025, 0.081, 0.101, 0.050, 0.022, 0.051, 0.043, 0.062, 0.054, 0.018, 0.031, 0.066
};
+/*
+MtArt model inserted in following
+
+7 Oct 2011 -- Lars Jermiin (lars.jermiin at csiro.au)
+*/
+
+/* MtArt: A New Model of Amino Acid Replacement for Arthropoda */
+/* Abascal, F., Posada, D., and Zardoya, R. 2007. Mol. Biol. Evol. 24:1-5. */
+static double mtartRelativeRates[NUM_AA_REL_RATES] = {
+ 0.19, 0.19, 0.59, 253.51, 0.19, 0.19, 199.84, 0.19, 25.69, 3.70, 0.19, 120.64, 13.10, 49.33, 672.97, 243.93, 0.19, 1.18, 339.91,
+ 0.19, 4.28, 35.51, 153.97, 0.19, 0.19, 41.30, 1.81, 1.77, 208.60, 5.18, 4.73, 0.19, 2.66, 0.19, 0.19, 3.88, 0.19,
+ 500.16, 98.18, 261.79, 183.04, 120.53, 179.54, 21.33, 12.65, 467.34, 78.81, 19.72, 16.54, 398.43, 165.89, 7.73, 251.17, 22.60,
+ 10.61, 0.19, 861.83, 12.46, 0.19, 6.60, 1.17, 1.68, 0.19, 0.19, 0.19, 44.35, 0.19, 0.19, 0.19, 0.19,
+ 0.19, 0.19, 80.53, 12.37, 63.00, 78.71, 0.19, 312.30, 184.06, 0.19, 664.16, 182.80, 21.61, 71.99, 350.40,
+ 261.55, 2.64, 313.50, 10.54, 16.28, 349.28, 67.33, 0.19, 39.30, 52.36, 43.68, 6.68, 86.67, 0.19,
+ 43.86, 15.25, 6.81, 1.72, 106.31, 0.19, 0.19, 7.88, 31.50, 43.40, 10.99, 7.74, 13.63,
+ 0.19, 2.74, 1.36, 0.19, 55.71, 0.83, 0.19, 226.03, 0.19, 1.88, 8.65, 2.56,
+ 0.19, 5.54, 0.19, 0.19, 13.78, 0.79, 10.62, 18.59, 0.19, 191.43, 0.19,
+ 514.54, 3.46, 514.78, 117.91, 0.19, 7.15, 203.74, 0.19, 12.33, 1854.52,
+ 3.78, 885.50, 262.57, 12.17, 8.17, 47.75, 21.13, 19.76, 84.72,
+ 105.61, 10.73, 16.82, 144.22, 69.54, 15.97, 117.09, 26.06,
+ 321.61, 5.26, 111.74, 288.57, 70.68, 70.92, 281.29,
+ 14.62, 36.05, 13.54, 53.67, 791.56, 51.90,
+ 86.50, 46.83, 0.19, 18.39, 31.70,
+ 660.39, 2.38, 30.45, 60.59,
+ 0.19, 45.98, 544.14,
+ 37.72, 0.19,
+ 1.59
+};
+
+static double mtartFrequencies[NUM_AA] = {
+ 0.054116, 0.018227, 0.039903, 0.020160, 0.009709, 0.018781, 0.024289, 0.068183, 0.024518, 0.092639, 0.148658, 0.021718, 0.061453, 0.088668, 0.041826, 0.091030, 0.049194, 0.029786, 0.039443, 0.057701
+};
+
/*************************************/
void SetAAModel(int theAAModel)
{
aaModel = theAAModel;
+/*
+"AA_MTART" inserted in position 6 of the following switch
+
+7 Oct 2011 -- Lars Jermiin (lars.jermiin at csiro.au)
+*/
switch (aaModel) {
case AA_JTT: SetRelativeRates(jttRelativeRates); break;
case AA_WAG: SetRelativeRates(wagRelativeRates); break;
@@ -248,10 +316,18 @@ void SetAAModel(int theAAModel)
case AA_BLOSUM62: SetRelativeRates(blosumRelativeRates); break;
case AA_MTREV24: SetRelativeRates(mtrevRelativeRates); break;
case AA_CPREV45: SetRelativeRates(cprevRelativeRates); break;
+ case AA_MTART: SetRelativeRates(mtartRelativeRates); break;
+ case AA_LG: SetRelativeRates(lgRelativeRates); break;
case AA_GENERAL:
// relative rates set by user
break;
}
+
+/*
+"AA_MTART" inserted in position 6 of the following switch
+
+7 Oct 2011 -- Lars Jermiin (lars.jermiin at csiro.au)
+*/
if (!aaFreqSet) {
switch (aaModel) {
@@ -261,6 +337,8 @@ void SetAAModel(int theAAModel)
case AA_BLOSUM62: SetFrequencies(blosumFrequencies); break;
case AA_MTREV24: SetFrequencies(mtrevFrequencies); break;
case AA_CPREV45: SetFrequencies(cprevFrequencies); break;
+ case AA_MTART: SetFrequencies(mtartFrequencies); break;
+ case AA_LG: SetFrequencies(lgFrequencies); break;
case AA_GENERAL:
// frequencies set by user
break;
diff --git a/source/aamodels.h b/source/aamodels.h
index 99c77b2..815d392 100755
--- a/source/aamodels.h
+++ b/source/aamodels.h
@@ -1,9 +1,9 @@
/* Header file for aamodels.c */
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -35,8 +35,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#ifndef _AA_MODELS_H_
@@ -49,7 +49,7 @@
#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_GENERAL, numAAModels };
+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;
diff --git a/source/eigen.c b/source/eigen.c
index df51bf4..4525c0f 100755
--- a/source/eigen.c
+++ b/source/eigen.c
@@ -1,16 +1,16 @@
/*
- Sequence Generator - seq-gen, version 1.3.2
+ Sequence Generator - seq-gen, version 1.3.3
Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
-
+ Institute of Evolutionary Biology, University of Edinburgh
+
The code in this file is taken from Ziheng Yang's PAML package.
http://abacus.gene.ucl.ac.uk/
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
-
+
#include <stdio.h>
#include <stdlib.h>
#include <time.h>
diff --git a/source/eigen.h b/source/eigen.h
index 3f8bf41..c23ac5c 100755
--- a/source/eigen.h
+++ b/source/eigen.h
@@ -1,16 +1,16 @@
/* Header file for eigen.c */
/*
- Sequence Generator - seq-gen, version 1.3.2
+ Sequence Generator - seq-gen, version 1.3.3
Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
-
+ Institute of Evolutionary Biology, University of Edinburgh
+
The code in this file is taken from Ziheng Yang's PAML package.
http://abacus.gene.ucl.ac.uk/
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#ifndef _EIGEN_H_
diff --git a/source/evolve.c b/source/evolve.c
index 18b1b60..559bdd5 100755
--- a/source/evolve.c
+++ b/source/evolve.c
@@ -1,7 +1,7 @@
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -33,8 +33,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#include <stdio.h>
@@ -76,6 +76,7 @@ void MutateSequence(char *seq, int inFromSite, int inNumSites, double len);
void SetSiteRates(int inFromSite, int inNumSites, double inScale);
void EvolveNode(TNode *anc, TNode *des, int inFromSite, int inNumSites, double scale);
+void WriteFastaFormat(FILE *fv, TTree **treeSet, int *partitionLengths);
void WritePhylipFormat(FILE *fv, TTree **treeSet, int *partitionLengths);
void WriteNexusFormat(FILE *fv, int treeNo, int datasetNo, TTree **treeSet, int *partitionLengths);
@@ -145,6 +146,11 @@ void SetCategories()
}
}
+/*
+Changed "j<numStates" to "j<numStates-1" in the following function to prevent array overflow
+
+20 October 2011 -- Michael Ott, CSIRO (michael.ott at csiro.au)
+*/
char SetState(double *P)
{
@@ -152,7 +158,7 @@ char SetState(double *P)
double r;
r=rndu();
- for (j=0; r>(*P) && j<numStates; j++) P++;
+ for (j=0; r>(*P) && j<numStates-1; j++) P++;
return j;
}
@@ -424,6 +430,9 @@ void WriteSequences(FILE *fv, int treeNo, int datasetNo, TTree **treeSet, int *p
case NEXUSFormat:
WriteNexusFormat(fv, treeNo, datasetNo, treeSet, partitionLengths);
break;
+ case FASTAFormat:
+ WriteFastaFormat(fv, treeSet, partitionLengths);
+ break;
}
}
@@ -461,6 +470,32 @@ void WritePhylipFormat(FILE *fv, TTree **treeSet, int *partitionLengths)
}
}
+void WriteFastaFormat(FILE *fv, TTree **treeSet, int *partitionLengths)
+{
+ size_t i, j, k;
+
+ for (i=0; i<numTaxa; i++) {
+ size_t printedSites = 0;
+
+ fprintf(fv, ">%s\n", treeSet[0]->names[i]);
+
+ for (j = 0; j < numPartitions; j++) {
+ char *P;
+ P=treeSet[j]->tips[i]->sequence;
+ for (k=0; k<partitionLengths[j]; k++) {
+ fputc(stateCharacters[(int)*P], fv);
+ P++;
+ if (++printedSites % 72 == 0) {
+ fputc('\n', fv);
+ }
+ }
+ }
+ if (printedSites % 72 != 0) {
+ fputc('\n', fv);
+ }
+ }
+}
+
void WriteNexusFormat(FILE *fv, int treeNo, int datasetNo, TTree **treeSet, int *partitionLengths)
{
int i, j, k, len, maxLen;
diff --git a/source/evolve.h b/source/evolve.h
index 18e503c..7f71fb5 100755
--- a/source/evolve.h
+++ b/source/evolve.h
@@ -1,9 +1,9 @@
/* Header file for evolve.c */
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -35,8 +35,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
@@ -63,7 +63,8 @@ enum {
enum {
PHYLIPFormat,
RelaxedFormat,
- NEXUSFormat
+ NEXUSFormat,
+ FASTAFormat
};
/* prototypes */
diff --git a/source/gamma.c b/source/gamma.c
index 2fe40bb..7d5f36e 100755
--- a/source/gamma.c
+++ b/source/gamma.c
@@ -1,14 +1,14 @@
/*
- Sequence Generator - seq-gen, version 1.3.2
+ Sequence Generator - seq-gen, version 1.3.3
Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
-
+ Institute of Evolutionary Biology, University of Edinburgh
+
The code in this file is taken from Ziheng Yang's PAML package.
http://abacus.gene.ucl.ac.uk/
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#include <math.h>
diff --git a/source/gamma.h b/source/gamma.h
index 93de839..a98bf60 100755
--- a/source/gamma.h
+++ b/source/gamma.h
@@ -1,16 +1,16 @@
/* Header file for gamma.c */
/*
- Sequence Generator - seq-gen, version 1.3.2
+ Sequence Generator - seq-gen, version 1.3.3
Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
-
+ Institute of Evolutionary Biology, University of Edinburgh
+
The code in this file is taken from Ziheng Yang's PAML package.
http://abacus.gene.ucl.ac.uk/
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#ifndef _GAMMA_H_
diff --git a/source/global.c b/source/global.c
index b931538..3739d44 100755
--- a/source/global.c
+++ b/source/global.c
@@ -1,7 +1,7 @@
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -33,8 +33,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#include <stdio.h>
diff --git a/source/global.h b/source/global.h
index 5a72881..16bdef2 100755
--- a/source/global.h
+++ b/source/global.h
@@ -1,9 +1,9 @@
/* Header file for global.c */
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -35,8 +35,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#ifndef _GLOBAL_H_
diff --git a/source/model.c b/source/model.c
index 3accbec..c148114 100755
--- a/source/model.c
+++ b/source/model.c
@@ -1,7 +1,7 @@
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -33,8 +33,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#include <stdio.h>
@@ -56,6 +56,8 @@ char *modelNames[numModels]={
"BLOSUM",
"MTREV",
"CPREV",
+ "MTART",
+ "LG",
"GENERAL"
};
@@ -69,6 +71,8 @@ char *modelTitles[numModels]={
"BLOSUM62: Henikoff & Henikoff (1992) PNAS USA 89:10915-10919",
"MTREV24: Adachi & Hasegawa (1996) J Mol Evol 42:459-468",
"CPREV45: Adachi et al. (2000) J Mol Evol 50:348-358",
+ "MTART: Abascal et al. (2007) Mol Biol Evol 24:1-5",
+ "LG: Le & Gascuel (2008) Mol Biol Evol 25:1307-1320",
"GENERAL: General time reversible (amino acids)"
};
diff --git a/source/model.h b/source/model.h
index 0927766..e3a755a 100755
--- a/source/model.h
+++ b/source/model.h
@@ -1,9 +1,9 @@
/* Header file for model.c */
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -35,8 +35,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#ifndef _MODEL_H_
@@ -44,7 +44,7 @@
extern char *stateCharacters;
-enum { NONE=-1, F84, HKY, GTR, JTT, WAG, PAM, BLOSUM, MTREV, CPREV, GENERAL, numModels };
+enum { NONE=-1, F84, HKY, GTR, JTT, WAG, PAM, BLOSUM, MTREV, CPREV, MTART, LG, GENERAL, numModels };
extern char *modelNames[numModels];
extern char *modelTitles[numModels];
diff --git a/source/nucmodels.c b/source/nucmodels.c
index 0bdec6b..7345b2b 100755
--- a/source/nucmodels.c
+++ b/source/nucmodels.c
@@ -1,7 +1,7 @@
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -33,8 +33,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#include <stdio.h>
diff --git a/source/nucmodels.h b/source/nucmodels.h
index e83af33..21d5568 100755
--- a/source/nucmodels.h
+++ b/source/nucmodels.h
@@ -1,9 +1,9 @@
/* Header file for nucmodels.c */
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -35,8 +35,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#ifndef _NUC_MODELS_H_
diff --git a/source/progress.c b/source/progress.c
index 38b06a7..e484294 100755
--- a/source/progress.c
+++ b/source/progress.c
@@ -1,7 +1,7 @@
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -33,8 +33,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#include <stdio.h>
diff --git a/source/progress.h b/source/progress.h
index af5f14d..b97d0ae 100755
--- a/source/progress.h
+++ b/source/progress.h
@@ -1,9 +1,9 @@
/* Header file for progress.c */
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -35,8 +35,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#ifndef _PROGRESS_H_
diff --git a/source/seq-gen.c b/source/seq-gen.c
index 70c8480..4372408 100755
--- a/source/seq-gen.c
+++ b/source/seq-gen.c
@@ -1,7 +1,7 @@
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -33,8 +33,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#include <stdio.h>
@@ -54,7 +54,7 @@
#include "twister.h"
#define PROGRAM_NAME "seq-gen"
-#define VERSION_NUMBER "Version 1.3.2"
+#define VERSION_NUMBER "Version 1.3.2x"
int treeFile, textFile, numDatasets, numTrees;
int scaleTrees, scaleBranches, ancestorSeq, writeAncestors, writeRates;
@@ -95,7 +95,7 @@ static void PrintTitle()
static void PrintUsage()
{
fprintf(stderr, "Usage: seq-gen [-m MODEL] [-l #] [-n #] [-p #] [-s # | -d #] [-k #]\n");
- fprintf(stderr, " [-c #1 #2 #3 | -a # [-g #]] [-f e | #] [-t # | -r #]\n");
+ fprintf(stderr, " [-c #1 #2 #3 | -a # [-g #]] [-i #] [-f e | #] [-t # | -r #]\n");
fprintf(stderr, " [-z #] [-o[p][r][n]] [-w[a][r]] [-x NAME] [-q] [-h] [treefile]\n");
fprintf(stderr, " -l: # = sequence length [default = 1000].\n");
fprintf(stderr, " -n: # = simulated datasets per tree [default = 1].\n");
@@ -105,13 +105,13 @@ static void PrintUsage()
fprintf(stderr, " -k: # = use sequence k as ancestral (needs alignment) [default = random].\n");
fprintf(stderr, "\n Substitution model options:\n");
- fprintf(stderr, " -m: MODEL = HKY, F84, GTR, JTT, WAG, PAM, BLOSUM, MTREV, GENERAL\n");
+ fprintf(stderr, " -m: MODEL = HKY, F84, GTR, JTT, WAG, PAM, BLOSUM, MTREV, CPREV45, MTART, LG, GENERAL\n");
fprintf(stderr, " HKY, F84 & GTR are for nucleotides the rest are for amino acids\n");
fprintf(stderr, " -a: # = shape (alpha) for gamma rate heterogeneity [default = none].\n");
fprintf(stderr, " -g: # = number of gamma rate categories [default = continuous].\n");
fprintf(stderr, " -i: # = proportion of invariable sites [default = 0.0].\n");
- fprintf(stderr, "\n Nucleotid model specific options:\n");
+ fprintf(stderr, "\n Nucleotide model specific options:\n");
fprintf(stderr, " -c: #1 #2 #3 = rates for codon position heterogeneity [default = none].\n");
fprintf(stderr, " -t: # = transition-transversion ratio [default = equal rate].\n");
fprintf(stderr, " -r: #1 #2 #3 #4 #5 #6= general rate matrix [default = all 1.0].\n");
@@ -128,6 +128,7 @@ static void PrintUsage()
fprintf(stderr, " p PHYLIP format\n");
fprintf(stderr, " r relaxed PHYLIP format\n");
fprintf(stderr, " n NEXUS format\n");
+ fprintf(stderr, " f FASTA format\n");
fprintf(stderr, " -w: Write additional information [default = none]\n");
fprintf(stderr, " a Write ancestral sequences for each node\n");
fprintf(stderr, " r Write rate for each site\n");
@@ -447,6 +448,7 @@ void ReadParams(int argc, char **argv)
case 'P': fileFormat=PHYLIPFormat; break;
case 'R': fileFormat=RelaxedFormat; break;
case 'N': fileFormat=NEXUSFormat; break;
+ case 'F': fileFormat=FASTAFormat; break;
default:
fprintf(stderr, "Unknown output format: %s\n\n", argv[i]);
PrintUsage();
diff --git a/source/tree.h b/source/tree.h
index 2d0113b..e1c564e 100755
--- a/source/tree.h
+++ b/source/tree.h
@@ -1,9 +1,9 @@
/* Header file to define tree and node structures */
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -35,8 +35,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#ifndef _TREE_H_
diff --git a/source/treefile.c b/source/treefile.c
index 90b46da..e42b597 100755
--- a/source/treefile.c
+++ b/source/treefile.c
@@ -1,7 +1,7 @@
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -33,8 +33,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#include <stdio.h>
@@ -127,6 +127,7 @@ TTree *NewTree()
strcpy(treeErrorMsg, "Out of memory creating tree.");
return NULL;
}
+ memset(tree, 0, sizeof(TTree)); /* grj */
tree->capacity=0;
CheckCapacity(tree, 1000);
@@ -161,8 +162,8 @@ void CheckCapacity(TTree *tree, int required)
newTips[i] = NULL;
}
- free(tree->names);
- free(tree->tips);
+ if (tree->names) { free(tree->names); tree->names=0; } /* grj */
+ if (tree->tips) { free(tree->tips); tree->tips = 0; } /* grj */
tree->names = newNames;
tree->tips = newTips;
@@ -313,7 +314,7 @@ TNode *ReadTip(FILE *fv, char ch, TTree *tree, int numNames, char **names)
}
*P='\0';
- CheckCapacity(tree, tree->numTips);
+ CheckCapacity(tree, tree->numTips+1);
if (numNames == 0) {
node->tipNo=tree->numTips;
diff --git a/source/treefile.h b/source/treefile.h
index 275d2ed..1e02fa4 100755
--- a/source/treefile.h
+++ b/source/treefile.h
@@ -1,9 +1,9 @@
/* Header file for treefile.c */
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -35,8 +35,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#ifndef _TREEFILE_H_
diff --git a/source/twister.c b/source/twister.c
index 860bc4d..07e90ca 100755
--- a/source/twister.c
+++ b/source/twister.c
@@ -1,14 +1,14 @@
/*
- Sequence Generator - seq-gen, version 1.3.2
- Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ 1996-2011, Andrew Rambaut & Nick Grassly
+ Institute of Evolutionary Biology, University of Edinburgh
The code in this file is covered by the license and copyright message
given below.
-
+
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
/*
diff --git a/source/twister.h b/source/twister.h
index 6d378c0..1e544b4 100755
--- a/source/twister.h
+++ b/source/twister.h
@@ -1,7 +1,9 @@
+/* Header file for twister.c */
+
/*
- Sequence Generator - seq-gen, version 1.3.2
- Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly
- Department of Zoology, University of Oxford
+ Sequence Generator - seq-gen, version 1.3.3
+ Copyright (c)1996-2011, 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
@@ -33,8 +35,8 @@
Any feedback is very welcome.
- http://evolve.zoo.ox.ac.uk/software/Seq-Gen/
- email: andrew.rambaut at zoo.ox.ac.uk
+ http://tree.bio.ed.ac.uk/software/seqgen/
+ email: a.rambaut at ed.ac.uk
*/
#ifndef _TWISTER_H_
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seq-gen.git
More information about the debian-med-commit
mailing list