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
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
|
WebLogo Release Notes
3.8 (2024-03-03) [Gavin Crooks, Melissa Fabros]
* fixes for Ghostscript deprecation
* remove support for python 3.8
Weblogo 3.8 runs under python 3.9, 3.10, 3.11, 3.12
3.7.11 (2022-05-26) [Gavin Crooks, Melissa Fabros]
* enable typehints
* updated examples for website
* `conda` installation enabled with `conda-forge`
* remove support for python 3.6
* Weblogo 3.7 runs under python 3.7, 3.8, 3.9 and 3.10
3.7 (2019-03-04) [Gavin Crooks]
* Refactor and cleanup code, removing python 2.7 support
* Extend API documentation
* WebLogo python package is now 'weblogo', rather than 'weblogolib',
matching pip install name. The 'corebio' package has been merged into 'weblogo'.
* Miscellaneous minor bug fixes and refactoring
* Weblogo 3.7 runs under python 3.6 and 3.7
3.6 (2017-12-29) [Gavin Crooks, Melissa Fabros]
* refactor version string creation
* update testing framework for use with tox and pytest
* weblogo is centered in it's png file (Kudos: Gert Huselmans)
* Miscellaneous minor bug fixes and refactoring (Kudos: Jerry Caskey, Coby Viner)
* fix headings in README.md
* Weblogo 3.6 runs under python 2.7, 3.4, 3.5 & 3.6
3.5 (2016-07-24) [Gavin Crooks, Melissa Fabros]
* Moved source control from GoogleCode to GitHub
* Switched from Subversion as version control method to Git
* Refactor html to optimize WebLogo use on mobile computing devices
* Add feature to open sequence files via file sharing URL link from Web application and command line
* Updated documentation
* PEP8ify all python files to solve formatting issues. (Kudos:Gert Hulselmans)
* Expose additonal LogoOptions via CLI options (Kudos:Gert Hulselmans)
* Fixed performance issue by limiting size of data that can be pasted into html form
Use file upload instead. (Kudos: Peter Cherepanov)
* Add ability to custom color every stack (Kudos: Kale Kundert)
* Weblogo 3.5 runs under python 2.6, 2.7, 3.2, 3.3, 3.4 & 3.5
* Fixed bugs for compatible with Python 3 (Kudos: Gert Hulselmans, Teshome Mulugeta)
* Miscellaneous minor bug fixes and refactoring (Kudos: David Kelley)
3.4 (2014-06-03) [Gavin Crooks, Eric Talevich]
* Python 3
Weblogo now runs under python 2.6, 2.7, 3.2, 3.3 & 3.4 (Python 2.5 is no longer
supported.) Note that the api for creating a logo has changed. See docs.
(Kudos: Eric Talevic)
* Fix bug with using Ghostscript 9.10 (Issue 36)
(Kudos: Michael Imbeault, Estienne Swart, FiReaNG3L)
* Fix various bugs in transfac parsing.
(Kudos: Promita Bose, Christopher Lamantia)
* Fix --complement of gapped sequences, added --revcomp option (Issue 36)
(Kudos: Jacob Engelbrecht)
* Miscellaneous minor bug fixes and refactoring.
(Kudos: Kamil Slowikowski, Jacob Engelbrecht)
3.3 (2012-07-02) [Gavin Crooks, David Sivak]
* Improved the algorithm that guesses the sequence type (DNA, RNA or protein)
(Kudos: Bug report, Roland Pache)
* Fixed an issue with reading transfac matrices with alternative alphabets
(Kudos: Bug report, Nima Emami)
* Fixed Motif.reindex()
* Implemented Motif.reverse() and Motif.complement()
(Can now reverse complement transfac matrix input on the command line.)
(Kudos: Feature request, Seth P Boudreaux)
* Command line interface now automagically recognizes transfac files.
* Add command line option "--reverse-stacks NO" which inverts the logo stacks
so that the most conserved monomers are at the bottom of the stack, rather than
the top. This ordering is consistent with the standard ordering for histograms,
and is arguably a better representation.
(Kudos: Luke Hutchison)
* Fixed an issue so that the correct color scheme is chosen
for the specified sequence type.
* Miscellaneous minor bug fixes and refactoring.
3.2 (2012-01-30) [Gavin Crooks, David Sivak]
* Graphical interface now accepts transfac format motif files.
* New output format option: SVG (Scalable Vector Graphics)
* Miscellaneous minor bug fixes and refactoring.
3.1 (2011-08-16) [Gavin Crooks, David Sivak]
Mostly bug fixes, code improvements and minor user enhancements.
* Command line: Add parsing of transfac PWM files
* Command line: Add reverse and complement transformations
* Improve clustal file parsing
* Currently compatible with python 2.5, 2.6 and 2.7
* Deprecate support for python 2.3 and 2.4
* Migrate corebio library into weblogo for easier maintenance and development.
* Add new annotate option for custom annotation line
* Miscellaneous minor bug fixes and refactoring.
* Incorporates bug fixes and feedback from Gavin Crooks, John Gilman,
Kevin Schutz and Perry Evan.
3.0 (2008-10-14) [GEC]
A significant update of WebLogo.
New and improved feature include:
* Simplified GUI. More useful options, less obscure options that are rarely
used.
* Several choices of unit including bits and nats, and corresponding energy
measures such as kJ/mol.
* Error bars are smaller and more discrete.
* The size of logo stacks is consistent (Does not change with sequence length.)
* The width of the characters in a stack are scaled by the fraction of non-gaps.
Therefore gappy columns are visually less important than columns with gaps.
* Three standard logo sizes.
* Can now read many multiple sequence alignment formats, including
CLUSTALW, FASTA, plain flatfile, MSF, NBRF, PIR, NEXUS and PHYLIP.
* High resolution PNG output.
* New, rational, easy to use command line client.
* Python based API library.
* New color schemes, including Watson-Crick pairing, hydrophobicity and charge.
* I (Isolucine) now shows crossbars, so that the letter is distinguishable
from a line.
* Colors can be specified using CSS2 syntax.
* Optional figure label.
* Conservation is now calculated as the Bayesian posterior mean relative
entropy. (This is the most significant change scientifically. The math
needed to get this right is very interesting.)
* Similarly, we now display Bayesian 95% confidence intervals for error bars.
* Compositional adjustment.
* Includes contributions from Clare Gollnick, David Ding, John Gilman.
* Incorporates bug fixes and feedback from John Reid, Gordon Robertson,
Eric Odell, Krisztina Gabor, ...
* Incorporates or adapts ideas and code from Gary Hon, Steven Brenner,
John-Marc Chandonia, Liana Lareau, Ed Green, James Casbon, Jeffrey Chang,
Frank Kauff, Cymon J. Cox, ...
-----------------------------------------------------------------------
2.8.2 (2005-09-08) [LL, GEC]
Various Bug fixes:
* Fixed Yellow (Was orange)
* Various improvements in handling malformed input.
* Fixed the fineprint checkbox option, which was stuck on.
* Renamed "Uniform Height Logo" option to a more descriptive
"Frequency Plot", and removed deceptive y-axis.
2.8.1 (2004-10-18) (Minor bug fix release) [GEC]
Bug fixes:
* Made weblogo compatibly with ghostscript version 8.1x.
This release is known to work with ghostscript version 7.05, 8.00 & 8.14
Kudos for bug reports and suggestions to:
* Lei Shen
2.8 (2004-10-01) [GEC]
Bug fixes:
* Fixed another form data parsing bug whose only apparent effect was to
fill up the webserver's error log.
* Fixed an issue with using double slashes in weblogo's url.
Kudos for bug reports and suggestions to:
* Eric Odell
* Scot Wolfe
* Alban Mancheron
* Ed Green
2.7 (2004-06-09) [GEC]
Bug fixes :
* Fixed logo.cgi's parsing of checkbox form data.
Kudos for bug reports and suggestions to:
* Eric Odell
2.6 (2004-03-15) [GEC, GH]
Bug fixes:
* Resolved an issue with hard coded paths within the
seqlogo command line client
* Improved the parsing of clustalw files
Kudos for bug reports and suggestions to:
* Allen Liu
* Guo Anyaun
* Harald Weber
2.5 (2004-02-19) [GEC, GH]
New features and enhancements :
* Added multiline logos.
2.4 (2004-01-29) [GEC, GH]
New features and enhancements :
* Added file upload for sequence data.
* Updated main page to reflect updated publication status
2.3 (2003-11-03) [GEC, GH]
New features and enhancements
* Added ability to parse CLUSTALW and flat file multiple sequence
alignment formats.
Bug fixes:
* Antialiasing PNGs now works with recent versions of ghostscript
* Can now change output file type when using Mozilla.
Kudos for bug reports and suggestions to:
* Stefanie Lager
* Ed Green
* Michael Galperin
2.2 (2003-08-01) [GEC, GH]
Several minor bug fixes and changes to the web pages.
* Fixed various buggy command line options
* A request for an empty yaxis label is now respected
* Fixed a major bug in temporary file name assignment
that prevented weblogo from running on some unix variants
New features and enhancements
* Made error bars darker
* Added option to control distance between tic marks
Kudos for bug reports and suggestions to
* Stefanie Lager
* Arlin Stoltzfus
* JP Cartailler
* Peter G. Warren
2.1 (2003-01-08) [GEC]
Several minor bug fixes and changes to the web pages.
2.0 (2002) [GEC, GH, JMC, SEB]
This second version of WebLogo is a complete rewrite of both
the user interface and the backend. Many new features and
options have been provided.
1.0 (1995) [SEB]
The original version of WebLogo was written in 1995 by Steven
Brenner, and was hosted by the School of Biological Science,
University of Cambridge
WebLogo change log
-----------------------
+ New feature
* Changed/Improved feature
! Fixed bug
- Removed feature
Versions : major.minor.patch.
The WebLogo Team
------------------
LL: Liana Lareau
GEC: Gavin E. Crooks
GH: Gary Hon
JMC: John-Marc Chandonia
SEB: Steven E. Brenner
|
