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<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom"><channel><title>Activity for Mauve</title><link>https://sourceforge.net/p/mauve/activity/</link><description>Recent activity for Mauve</description><language>en</language><lastBuildDate>Thu, 09 Oct 2025 14:35:24 -0000</lastBuildDate><item><title>Sara Moussadeq posted a comment on ticket #63</title><link>https://sourceforge.net/p/mauve/bugs/63/?limit=25#2f71</link><description>This didn't resolve the problem for me. I resolve the problem by using : conda install bioconda/label/cf201901::mauvealigner</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Sara Moussadeq</dc:creator><pubDate>Thu, 09 Oct 2025 14:35:24 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/63/?limit=25#2f71</guid></item><item><title>Yong Yang created ticket #66</title><link>https://sourceforge.net/p/mauve/bugs/66/</link><description>Exited with error code: 3</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Yong Yang</dc:creator><pubDate>Wed, 10 Aug 2022 02:18:02 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/66/</guid></item><item><title>Yong Yang created ticket #65</title><link>https://sourceforge.net/p/mauve/bugs/65/</link><description>mauve is not running</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Yong Yang</dc:creator><pubDate>Thu, 30 Jun 2022 05:46:07 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/65/</guid></item><item><title>Daniel Vieira da Silva created ticket #26</title><link>https://sourceforge.net/p/mauve/feature-requests/26/</link><description>Caught signal 11</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Daniel Vieira da Silva</dc:creator><pubDate>Wed, 24 Feb 2021 20:01:23 -0000</pubDate><guid>https://sourceforge.net/p/mauve/feature-requests/26/</guid></item><item><title>Oren Milman posted a comment on ticket #64</title><link>https://sourceforge.net/p/mauve/bugs/64/?limit=25#eae1</link><description>I have created the ticket twice accidentally (on the first time, sourceforge told me that creating the ticket failed). I apologize. Please close (or delete, if possible) this duplicate.</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Oren Milman</dc:creator><pubDate>Thu, 10 Dec 2020 17:33:01 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/64/?limit=25#eae1</guid></item><item><title>Oren Milman created ticket #63</title><link>https://sourceforge.net/p/mauve/bugs/63/</link><description>a workaround for mauveAligner: symbol lookup error: mauveAligner: undefined symbol: _ZN6genome10gnSequence10LoadSourceESs</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Oren Milman</dc:creator><pubDate>Thu, 10 Dec 2020 17:30:06 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/63/</guid></item><item><title>Oren Milman created ticket #64</title><link>https://sourceforge.net/p/mauve/bugs/64/</link><description>a workaround for mauveAligner: symbol lookup error: mauveAligner: undefined symbol: _ZN6genome10gnSequence10LoadSourceESs</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Oren Milman</dc:creator><pubDate>Thu, 10 Dec 2020 17:28:01 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/64/</guid></item><item><title>Gizem Avcı created ticket #62</title><link>https://sourceforge.net/p/mauve/bugs/62/</link><description>Thread-7</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Gizem Avcı</dc:creator><pubDate>Mon, 16 Nov 2020 19:14:07 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/62/</guid></item><item><title>Devina Bhookhun-Seeruttun created ticket #61</title><link>https://sourceforge.net/p/mauve/bugs/61/</link><description>Caught signal 11</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Devina Bhookhun-Seeruttun</dc:creator><pubDate>Mon, 07 Sep 2020 02:34:16 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/61/</guid></item><item><title>Ann Gill posted a comment on ticket #56</title><link>https://sourceforge.net/p/mauve/bugs/56/?limit=25#496e</link><description>I have the same problem-- macOS Catalina v 10.15.4</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Ann Gill</dc:creator><pubDate>Thu, 04 Jun 2020 18:15:40 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/56/?limit=25#496e</guid></item><item><title>Ekaterina Bocharova posted a comment on ticket #56</title><link>https://sourceforge.net/p/mauve/bugs/56/?limit=25#fd6e</link><description>Hi! I have the same error: gnDefs.cpp:8:7: error: 'abs' is missing exception specification 'throw()' int64 abs( int64 a ){ ^ throw() /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/stdlib.h:113:44: note: previous declaration is here inline _LIBCPP_INLINE_VISIBILITY long long abs(long long __x) _NOEXCEPT ... ^ 1 error generated. make[1]: [gnDefs.lo] Error 1 make[1]: Waiting for unfinished jobs.... make: *** [install-recursive] Error 1 I'm compiling...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Ekaterina Bocharova</dc:creator><pubDate>Wed, 04 Mar 2020 12:30:34 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/56/?limit=25#fd6e</guid></item><item><title>Anthony Einfeldt created ticket #60</title><link>https://sourceforge.net/p/mauve/bugs/60/</link><description>Viewer stuck reading file</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Anthony Einfeldt</dc:creator><pubDate>Thu, 12 Dec 2019 15:28:01 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/60/</guid></item><item><title>printer error created ticket #59</title><link>https://sourceforge.net/p/mauve/bugs/59/</link><description>java visualization errors</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">printer error</dc:creator><pubDate>Wed, 11 Dec 2019 17:34:48 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/59/</guid></item><item><title>John Joe posted a comment on ticket #58</title><link>https://sourceforge.net/p/mauve/bugs/58/?limit=25#f660</link><description>That's weird - as far as I can tell the stream never closes itself until the program exits so output.flush() should have had the same effect. I had a similar problem a few days before you posted your issue where the file was not completely written and added output.flush() using a different method which solved it for me. The code is convoluted so I might be missing something. Well, as long as it eventually ended up working it's fine I guess.</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">John Joe</dc:creator><pubDate>Fri, 23 Aug 2019 17:41:21 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/58/?limit=25#f660</guid></item><item><title>andrew davis posted a comment on ticket #58</title><link>https://sourceforge.net/p/mauve/bugs/58/?limit=25#a094</link><description>Just FYI I changed: line 133 output.flush(); -&gt; output.close(); The file was closing before it was done writing.</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">andrew davis</dc:creator><pubDate>Fri, 23 Aug 2019 16:22:12 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/58/?limit=25#a094</guid></item><item><title>andrew davis posted a comment on ticket #58</title><link>https://sourceforge.net/p/mauve/bugs/58/?limit=25#8a58</link><description>Thanks John! That helped. I had to run: jar cf Mauve-2.jar ext images org</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">andrew davis</dc:creator><pubDate>Wed, 21 Aug 2019 13:53:16 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/58/?limit=25#8a58</guid></item><item><title>John Joe modified a comment on ticket #58</title><link>https://sourceforge.net/p/mauve/bugs/58/?limit=25#8c78</link><description>I can't help you much with #1 since I never tried building from source myself, but for #2 make sure you still have the other necessary libraries in their proper place - your error isn't a version error but a "I can't find the stuff this program relies on error" Specifically, the file/folder layout should be (relative to Mauve.jar's directory) ./Mauve.jar ./ext/bytecode-1.9.2-SNAPSHOT.jar ./ext/commons-cli-1.2.jar ./ext/core-1.9.2-SNAPSHOT.jar ./ext/gui-1.9.2-SNAPSHOT.jar These libraries should have...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">John Joe</dc:creator><pubDate>Tue, 20 Aug 2019 19:47:56 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/58/?limit=25#8c78</guid></item><item><title>John Joe posted a comment on ticket #58</title><link>https://sourceforge.net/p/mauve/bugs/58/?limit=25#8c78</link><description>I can't help you much with #1 since I never tried building from source myself, but for #2 make sure you still have the other necessary libraries in their proper place - your error isn't a version error but a "I can't find the stuff this program relies on error" Specifically, the file/folder layout should be (relative to Mauve.jar's directory) ./Mauve.jar ./ext/bytecode-1.9.2-SNAPSHOT.jar ./ext/commons-cli-1.2.jar ./ext/core-1.9.2-SNAPSHOT.jar ./ext/gui-1.9.2-SNAPSHOT.jar</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">John Joe</dc:creator><pubDate>Tue, 20 Aug 2019 19:45:50 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/58/?limit=25#8c78</guid></item><item><title>andrew davis posted a comment on ticket #58</title><link>https://sourceforge.net/p/mauve/bugs/58/?limit=25#5472</link><description>Thanks John for the quick reponse. I tried doing a fresh build in a docker container, following the build instructions (http://darlinglab.org/mauve/developer-guide/building.html) ran into a Makefile error: Makefile:761: recipe for target 'Aligner.lo' failed make[1]: [Aligner.lo] Error 1 make[1]: Leaving directory '/root/build/libMems/libMems' Makefile:546: recipe for target 'install-recursive' failed make: [install-recursive] Error 1 compiled SnpExporter.java into org/gel/mauve/analysis/ and re-created...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">andrew davis</dc:creator><pubDate>Tue, 20 Aug 2019 19:16:48 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/58/?limit=25#5472</guid></item><item><title>John Joe posted a comment on ticket #58</title><link>https://sourceforge.net/p/mauve/bugs/58/?limit=25#1d85</link><description>Hello, I'm not the developer, but I think I know may know what is happening: If you downloaded it directly from the website (development snapshot 2015-02-26, or really any version that is older than the latest revision r4736 (made on 2016-06-08), using the SnpExporter may result in an incomplete output file. Your choices are: 1. Build Mauve from source 2. Take the code from https://sourceforge.net/p/mauve/code/HEAD/tree//mauve/trunk/src/org/gel/mauve/analysis/SnpExporter.java, compile it, so you...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">John Joe</dc:creator><pubDate>Tue, 20 Aug 2019 15:57:14 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/58/?limit=25#1d85</guid></item><item><title>andrew davis created ticket #58</title><link>https://sourceforge.net/p/mauve/bugs/58/</link><description>Snp file from a command line</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">andrew davis</dc:creator><pubDate>Tue, 20 Aug 2019 15:05:47 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/58/</guid></item><item><title>Jarrett F. Lebov created ticket #57</title><link>https://sourceforge.net/p/mauve/bugs/57/</link><description>Exited with error code: -1073741676</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jarrett F. Lebov</dc:creator><pubDate>Sat, 23 Mar 2019 22:47:25 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/57/</guid></item><item><title>Marius Walter created ticket #56</title><link>https://sourceforge.net/p/mauve/bugs/56/</link><description>Error when compiling </description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Marius Walter</dc:creator><pubDate>Fri, 28 Sep 2018 17:07:46 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/56/</guid></item><item><title>Pat created ticket #55</title><link>https://sourceforge.net/p/mauve/bugs/55/</link><description>Score an assembly Error</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Pat</dc:creator><pubDate>Tue, 04 Sep 2018 11:26:04 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/55/</guid></item><item><title>Yaser Alsahafi posted a comment on ticket #52</title><link>https://sourceforge.net/p/mauve/bugs/52/?limit=25#012d</link><description>I faced the same problem when aligning multiple genomes in .gb format. However, I was able to overcome it be using only on file in .gb format, which was my reference genome, and the other files in .fasta format. This was I was ablt to compute the DJC distance. I tried to contact the email listed in the erorr, but did get any response. In interpretation, I hope somebody could help in resolving this issue.</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Yaser Alsahafi</dc:creator><pubDate>Fri, 03 Aug 2018 20:03:40 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/52/?limit=25#012d</guid></item><item><title>Kazi Ahsan created ticket #54</title><link>https://sourceforge.net/p/mauve/bugs/54/</link><description>Mauve Contig Mover: getting error while  reordering  genbank output</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Kazi Ahsan</dc:creator><pubDate>Wed, 27 Jun 2018 17:42:13 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/54/</guid></item><item><title>James Abbott created ticket #53</title><link>https://sourceforge.net/p/mauve/bugs/53/</link><description>Additional header required for recent boost versions</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">James Abbott</dc:creator><pubDate>Tue, 19 Jun 2018 13:48:10 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/53/</guid></item><item><title>seshank created ticket #52</title><link>https://sourceforge.net/p/mauve/bugs/52/</link><description>DCJ rearrangement analysis error</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">seshank</dc:creator><pubDate>Tue, 19 Jun 2018 10:37:30 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/52/</guid></item><item><title>Harry Pickering created ticket #51</title><link>https://sourceforge.net/p/mauve/bugs/51/</link><description>progressivemauve sequences missing from output</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Harry Pickering</dc:creator><pubDate>Mon, 15 Jan 2018 09:49:31 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/51/</guid></item><item><title>Jessie created ticket #50</title><link>https://sourceforge.net/p/mauve/bugs/50/</link><description>Mauve Error 134 with move contigs</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jessie</dc:creator><pubDate>Tue, 21 Nov 2017 19:48:39 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/50/</guid></item><item><title>Elham Elkrewi created ticket #25</title><link>https://sourceforge.net/p/mauve/feature-requests/25/</link><description>error code 3</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Elham Elkrewi</dc:creator><pubDate>Wed, 02 Aug 2017 13:20:00 -0000</pubDate><guid>https://sourceforge.net/p/mauve/feature-requests/25/</guid></item><item><title>Thomas Rattei created ticket #49</title><link>https://sourceforge.net/p/mauve/bugs/49/</link><description>Alignment errors or missing annotations when using gbk files from RefSeq</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Thomas Rattei</dc:creator><pubDate>Thu, 27 Jul 2017 10:11:13 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/49/</guid></item><item><title>Bhavya Papudeshi created ticket #48</title><link>https://sourceforge.net/p/mauve/bugs/48/</link><description>Cant look up annotation features when using a genbank file (.gbk)</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Bhavya Papudeshi</dc:creator><pubDate>Mon, 24 Jul 2017 17:42:18 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/48/</guid></item><item><title>Yongan posted a comment on ticket #47</title><link>https://sourceforge.net/p/mauve/bugs/47/?limit=25#21f0</link><description>I found there are RC sequences. My bad. Please close the ticket!</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Yongan</dc:creator><pubDate>Fri, 20 Jan 2017 18:56:05 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/47/?limit=25#21f0</guid></item><item><title>Yongan created ticket #47</title><link>https://sourceforge.net/p/mauve/bugs/47/</link><description>concatenated block sequences are different from original sequences</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Yongan</dc:creator><pubDate>Thu, 12 Jan 2017 23:14:47 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/47/</guid></item><item><title>Gert Wollny created ticket #46</title><link>https://sourceforge.net/p/mauve/bugs/46/</link><description>libMems does not compile with g++-6 [patch]</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Gert Wollny</dc:creator><pubDate>Thu, 30 Jun 2016 13:36:21 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/46/</guid></item><item><title>Aaron Darling committed [r4736]</title><link>https://sourceforge.net/p/mauve/code/4736/</link><description>need to flush the output buffer!</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Wed, 08 Jun 2016 22:19:47 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4736/</guid></item><item><title>Anirvan Chatterjee posted a comment on ticket #45</title><link>https://sourceforge.net/p/mauve/bugs/45/?limit=25#7e64/ba06</link><description>Dear Aaron, thank you for your reply. The duplication was an error. However rectifying...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Anirvan Chatterjee</dc:creator><pubDate>Tue, 24 May 2016 05:17:01 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/45/?limit=25#7e64/ba06</guid></item><item><title>Aaron Darling posted a comment on ticket #45</title><link>https://sourceforge.net/p/mauve/bugs/45/?limit=25#7e64</link><description>It looks like progressiveMauve is unable to open the first sequence file. I notice...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Sun, 22 May 2016 23:17:35 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/45/?limit=25#7e64</guid></item><item><title>Anirvan Chatterjee created ticket #45</title><link>https://sourceforge.net/p/mauve/bugs/45/</link><description>eror 136</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Anirvan Chatterjee</dc:creator><pubDate>Wed, 18 May 2016 11:56:46 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/45/</guid></item><item><title>Fabrice Touzain created ticket #44</title><link>https://sourceforge.net/p/mauve/bugs/44/</link><description>No contig names display in Mauve GUI on Windows 7 when reading a xmfa file</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Fabrice Touzain</dc:creator><pubDate>Mon, 08 Feb 2016 08:59:25 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/44/</guid></item><item><title>Aaron Darling committed [r4735]</title><link>https://sourceforge.net/p/mauve/code/4735/</link><description>remove unimplemented --input-id-matrix option (...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Tue, 13 Oct 2015 22:37:39 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4735/</guid></item><item><title>Ivan Alexandrov created ticket #43</title><link>https://sourceforge.net/p/mauve/bugs/43/</link><description>Mauve error code 139</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Ivan Alexandrov</dc:creator><pubDate>Mon, 08 Jun 2015 10:44:05 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/43/</guid></item><item><title>Cristina created ticket #42</title><link>https://sourceforge.net/p/mauve/bugs/42/</link><description>trouble with contig coordinates in the backbone file</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Cristina</dc:creator><pubDate>Thu, 14 May 2015 19:53:38 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/42/</guid></item><item><title>Joaquim Martins Jr created ticket #41</title><link>https://sourceforge.net/p/mauve/bugs/41/</link><description>progressiveMauve2.3.1 error</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Joaquim Martins Jr</dc:creator><pubDate>Mon, 06 Apr 2015 19:28:36 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/41/</guid></item><item><title>thekswenson posted a comment on ticket #40</title><link>https://sourceforge.net/p/mauve/bugs/40/?limit=25#b01c/d217</link><description>Hi Aaron, I am using 2.3.1build1! Sorry about that... I should have checked for a...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">thekswenson</dc:creator><pubDate>Thu, 02 Apr 2015 08:20:22 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/40/?limit=25#b01c/d217</guid></item><item><title>Aaron Darling posted a comment on ticket #40</title><link>https://sourceforge.net/p/mauve/bugs/40/?limit=25#b01c</link><description>Hi Krister, looks like you're on linux, do you know which JVM version you've got...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Thu, 02 Apr 2015 03:53:39 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/40/?limit=25#b01c</guid></item><item><title>krumplestiltskin created ticket #40</title><link>https://sourceforge.net/p/mauve/bugs/40/</link><description>"align" button off window boarder</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">krumplestiltskin</dc:creator><pubDate>Wed, 01 Apr 2015 13:49:42 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/40/</guid></item><item><title>Aaron Darling committed [r4734]</title><link>https://sourceforge.net/p/mauve/code/4734/</link><description>enable selection of multiple sequence files at ...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Tue, 31 Mar 2015 01:55:15 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4734/</guid></item><item><title>Aaron Darling committed [r4733]</title><link>https://sourceforge.net/p/mauve/code/4733/</link><description>Change defaults to compensate for triplet indel...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Tue, 10 Mar 2015 05:34:58 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4733/</guid></item><item><title>Aaron Darling committed [r4732]</title><link>https://sourceforge.net/p/mauve/code/4732/</link><description>Fix to triplet indel bias</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Tue, 10 Mar 2015 05:34:06 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4732/</guid></item><item><title>Aaron Darling committed [r4731]</title><link>https://sourceforge.net/p/mauve/code/4731/</link><description>disconnect testing command line</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Mon, 09 Mar 2015 05:20:52 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4731/</guid></item><item><title>Aaron Darling committed [r4730]</title><link>https://sourceforge.net/p/mauve/code/4730/</link><description>fixes for linux build</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Mon, 09 Mar 2015 04:42:08 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4730/</guid></item><item><title>Aaron Darling committed [r4729]</title><link>https://sourceforge.net/p/mauve/code/4729/</link><description>Changes to introduce gene-awareness and elimina...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Mon, 09 Mar 2015 04:28:47 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4729/</guid></item><item><title>Aaron Darling committed [r4728]</title><link>https://sourceforge.net/p/mauve/code/4728/</link><description>enable allocation of histograms smaller than th...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Tue, 03 Mar 2015 04:17:29 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4728/</guid></item><item><title>Aaron Darling committed [r4727]</title><link>https://sourceforge.net/p/mauve/code/4727/</link><description>updated with new deployment address</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Fri, 27 Feb 2015 04:23:21 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4727/</guid></item><item><title>norhan mahfouz created ticket #39</title><link>https://sourceforge.net/p/mauve/bugs/39/</link><description>Mauve aligner without SML files</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">norhan mahfouz</dc:creator><pubDate>Thu, 26 Feb 2015 13:04:47 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/39/</guid></item><item><title>Aaron Darling committed [r4726]</title><link>https://sourceforge.net/p/mauve/code/4726/</link><description>update with new target name</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Wed, 25 Feb 2015 02:48:11 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4726/</guid></item><item><title>Aaron Darling committed [r4725]</title><link>https://sourceforge.net/p/mauve/code/4725/</link><description>workaround for boost memory mapped file corrupt...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Fri, 13 Feb 2015 05:38:27 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4725/</guid></item><item><title>Aaron Darling posted a comment on ticket #38</title><link>https://sourceforge.net/p/mauve/bugs/38/?limit=25#c9eb/5edc/bb78/b643/3e92</link><description>Hi Sarah, your attachment didn't show up. I would suggest reading this page to understand...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Mon, 19 Jan 2015 03:43:30 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/38/?limit=25#c9eb/5edc/bb78/b643/3e92</guid></item><item><title>Sarah posted a comment on ticket #38</title><link>https://sourceforge.net/p/mauve/bugs/38/?limit=25#c9eb/5edc/bb78/b643</link><description>Hi Aaron, I've been looking over the .backbone file (attached) but I'm seeing negative...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Sarah</dc:creator><pubDate>Fri, 16 Jan 2015 18:20:19 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/38/?limit=25#c9eb/5edc/bb78/b643</guid></item><item><title>Aaron Darling posted a comment on ticket #38</title><link>https://sourceforge.net/p/mauve/bugs/38/?limit=25#c9eb/5edc/bb78</link><description>Thanks Sarah, I'll check out that code. In the meantime, I suggest you have a look...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Fri, 16 Jan 2015 02:29:28 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/38/?limit=25#c9eb/5edc/bb78</guid></item><item><title>Sarah posted a comment on ticket #38</title><link>https://sourceforge.net/p/mauve/bugs/38/?limit=25#c9eb/5edc</link><description>You're correct, the format of the text is output from a code I found in a publication....</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Sarah</dc:creator><pubDate>Fri, 16 Jan 2015 02:15:31 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/38/?limit=25#c9eb/5edc</guid></item><item><title>Aaron Darling posted a comment on ticket #38</title><link>https://sourceforge.net/p/mauve/bugs/38/?limit=25#c9eb</link><description>Hi Sarah, the text screenshot does not appear to correspond to an XMFA file. Could...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Fri, 16 Jan 2015 01:27:27 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/38/?limit=25#c9eb</guid></item><item><title>Sarah created ticket #38</title><link>https://sourceforge.net/p/mauve/bugs/38/</link><description>GUI vs XMFA Text File</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Sarah</dc:creator><pubDate>Thu, 15 Jan 2015 22:15:21 -0000</pubDate><guid>https://sourceforge.net/p/mauve/bugs/38/</guid></item><item><title>Aaron Darling committed [r4724]</title><link>https://sourceforge.net/p/mauve/code/4724/</link><description>bugfix</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Mon, 12 Jan 2015 01:51:26 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4724/</guid></item><item><title>Aaron Darling committed [r4723]</title><link>https://sourceforge.net/p/mauve/code/4723/</link><description>build with -O0 until clang/llvm bug with except...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Mon, 12 Jan 2015 01:45:26 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4723/</guid></item><item><title>Aaron Darling committed [r4722]</title><link>https://sourceforge.net/p/mauve/code/4722/</link><description>update snapshots to new web host</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Fri, 09 Jan 2015 00:26:02 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4722/</guid></item><item><title>Aaron Darling committed [r4721]</title><link>https://sourceforge.net/p/mauve/code/4721/</link><description>ant build now requires java 7</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Mon, 22 Dec 2014 01:45:58 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4721/</guid></item><item><title>Aaron Darling committed [r4720]</title><link>https://sourceforge.net/p/mauve/code/4720/</link><description>updated binaries and build for 2.4.0 release</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Mon, 22 Dec 2014 01:43:50 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4720/</guid></item><item><title>Aaron Darling committed [r4719]</title><link>https://sourceforge.net/p/mauve/code/4719/</link><description>update to current repository and server location</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Mon, 22 Dec 2014 00:56:48 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4719/</guid></item><item><title>Aaron Darling committed [r4718]</title><link>https://sourceforge.net/p/mauve/code/4718/</link><description>updated to deploy to new server</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Mon, 22 Dec 2014 00:45:46 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4718/</guid></item><item><title>Aaron Darling committed [r4717]</title><link>https://sourceforge.net/p/mauve/code/4717/</link><description>potential fix for msvc compiler error</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Sun, 21 Dec 2014 06:59:59 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4717/</guid></item><item><title>Aaron Darling committed [r4716]</title><link>https://sourceforge.net/p/mauve/code/4716/</link><description>fix for windows build</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Sun, 21 Dec 2014 06:57:45 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4716/</guid></item><item><title>Aaron Darling committed [r4715]</title><link>https://sourceforge.net/p/mauve/code/4715/</link><description>need to copy with ditto to preserve executable ...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Fri, 19 Dec 2014 02:58:48 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4715/</guid></item><item><title>Aaron Darling committed [r4714]</title><link>https://sourceforge.net/p/mauve/code/4714/</link><description>binaries for 2.4.0 release, taken from the 2012...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Fri, 19 Dec 2014 02:57:20 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4714/</guid></item><item><title>Aaron Darling committed [r4713]</title><link>https://sourceforge.net/p/mauve/code/4713/</link><description>improved error message when output file is unwr...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Wed, 17 Dec 2014 08:09:00 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4713/</guid></item><item><title>Aaron Darling committed [r4712]</title><link>https://sourceforge.net/p/mauve/code/4712/</link><description>bugfix</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Wed, 17 Dec 2014 04:24:21 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4712/</guid></item><item><title>Aaron Darling committed [r4711]</title><link>https://sourceforge.net/p/mauve/code/4711/</link><description>fix typo</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Wed, 17 Dec 2014 03:55:30 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4711/</guid></item><item><title>Aaron Darling committed [r4710]</title><link>https://sourceforge.net/p/mauve/code/4710/</link><description>revisions for more robust build system</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Wed, 17 Dec 2014 03:52:21 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4710/</guid></item><item><title>Aaron Darling committed [r4709]</title><link>https://sourceforge.net/p/mauve/code/4709/</link><description>workaround for strange behavior with boost 1.57...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Wed, 17 Dec 2014 03:02:48 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4709/</guid></item><item><title>Aaron Darling committed [r4708]</title><link>https://sourceforge.net/p/mauve/code/4708/</link><description>add java runtime to OS X build, other refinements</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Wed, 17 Dec 2014 02:56:55 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4708/</guid></item><item><title>Aaron Darling committed [r4707]</title><link>https://sourceforge.net/p/mauve/code/4707/</link><description>include rt.jar from java 1.6 in bootclasspath t...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Wed, 17 Dec 2014 01:08:39 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4707/</guid></item><item><title>Aaron Darling committed [r4706]</title><link>https://sourceforge.net/p/mauve/code/4706/</link><description>use svn urls instead of http</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Tue, 16 Dec 2014 11:43:11 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4706/</guid></item><item><title>Aaron Darling committed [r4705]</title><link>https://sourceforge.net/p/mauve/code/4705/</link><description>DeMaere special request: improved responsivenes...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Tue, 16 Dec 2014 10:12:33 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4705/</guid></item><item><title>Aaron Darling committed [r4704]</title><link>https://sourceforge.net/p/mauve/code/4704/</link><description>updates to os X disk image packaging</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Tue, 16 Dec 2014 05:06:20 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4704/</guid></item><item><title>Aaron Darling committed [r4703]</title><link>https://sourceforge.net/p/mauve/code/4703/</link><description>move empty check further down to allow empty ob...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Tue, 16 Dec 2014 02:43:09 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4703/</guid></item><item><title>Aaron Darling committed [r4702]</title><link>https://sourceforge.net/p/mauve/code/4702/</link><description>don't keep changelog in mauve repo, master copy...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Tue, 16 Dec 2014 02:40:22 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4702/</guid></item><item><title>Aaron Darling committed [r4701]</title><link>https://sourceforge.net/p/mauve/code/4701/</link><description>re-add shell script, prep for 2.4.0 release</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Tue, 16 Dec 2014 02:39:14 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4701/</guid></item><item><title>Aaron Darling committed [r4700]</title><link>https://sourceforge.net/p/mauve/code/4700/</link><description>updating classpath to include latest biojava</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Tue, 16 Dec 2014 02:38:10 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4700/</guid></item><item><title>Aaron Darling committed [r4699]</title><link>https://sourceforge.net/p/mauve/code/4699/</link><description>removing 32-bit support</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Tue, 16 Dec 2014 02:18:16 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4699/</guid></item><item><title>Aaron Darling committed [r4698]</title><link>https://sourceforge.net/p/mauve/code/4698/</link><description>custom biojava with parsing fix for Prokka-gene...</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Tue, 16 Dec 2014 02:13:08 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4698/</guid></item><item><title>Aaron Darling committed [r4697]</title><link>https://sourceforge.net/p/mauve/code/4697/</link><description>updates for server migration</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Mon, 15 Dec 2014 10:02:59 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4697/</guid></item><item><title>Aaron Darling committed [r4696]</title><link>https://sourceforge.net/p/mauve/code/4696/</link><description>drop linux 32 bit support </description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Sun, 14 Dec 2014 23:11:18 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4696/</guid></item><item><title>Aaron Darling committed [r4695]</title><link>https://sourceforge.net/p/mauve/code/4695/</link><description>update biojava to 1.9.1 release</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Sat, 13 Dec 2014 06:53:03 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4695/</guid></item><item><title>Aaron Darling committed [r4694]</title><link>https://sourceforge.net/p/mauve/code/4694/</link><description>fix for OS X binary path problem</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Fri, 12 Dec 2014 05:23:20 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4694/</guid></item><item><title>Aaron Darling committed [r4693]</title><link>https://sourceforge.net/p/mauve/code/4693/</link><description>site migration, clean some OS X cruft</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Fri, 12 Dec 2014 05:05:03 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4693/</guid></item><item><title>Aaron Darling committed [r4692]</title><link>https://sourceforge.net/p/mauve/code/4692/</link><description>Fix off-by-one, clean up some cruft</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Fri, 12 Dec 2014 04:35:08 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4692/</guid></item><item><title>Aaron Darling committed [r4691]</title><link>https://sourceforge.net/p/mauve/code/4691/</link><description>switch to platform-specific command keys</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Aaron Darling</dc:creator><pubDate>Fri, 12 Dec 2014 04:33:05 -0000</pubDate><guid>https://sourceforge.net/p/mauve/code/4691/</guid></item></channel></rss>