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From: VALAT C. <Cha...@an...> - 2015-03-17 13:14:34
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Dear all, I'm a new user of Mauve and I have problems with "move contigs" tool. The application stops and the error code on the console is : progressiveMauve --output=C:\Users\c.valat\Desktop\reordering\alignment1\alignment1 --skip-refinement --weight=200 --output-guide-tree=C:\Users\c.valat\Desktop\reordering\alignment1\alignment1.guide_tree --backbone-output=C:\Users\c.valat\Desktop\reordering\alignment1\alignment1.backbone C:\Users\c.valat\Desktop\reordering\alignment1\pO26GQ25988.1.txt C:\Users\c.valat\Desktop\reordering\alignment1\Escherichia_coli_aSTEC19352.not_aligned.fasta Storing raw sequence at C:\Users\C3214~1.VAL\AppData\Local\Temp\rawD89.tmp Sequence loaded successfully. C:\Users\c.valat\Desktop\reordering\alignment1\pO26GQ25988.1.txt 111481 base pairs. Storing raw sequence at C:\Users\C3214~1.VAL\AppData\Local\Temp\rawD99.tmp Sequence loaded successfully. C:\Users\c.valat\Desktop\reordering\alignment1\Escherichia_coli_aSTEC19352.not_aligned.fasta 584721 base pairs. Using weight 13 mers for initial seeds Creating sorted mer list Create time was: 0 seconds. Creating sorted mer list Create time was: 0 seconds. 1%..2%..4%..5%..7%..8%..10%.. 11%..12%..14%..15%..17%..18%..20%.. 21%..22%..24%..25%..27%..28%..30%.. 31%..33%..34%..35%..37%..38%..40%.. 41%..43%..44%..45%..47%..48%..50%.. 51%..53%..54%..56%..57%..58%..60%.. 61%..63%..64%..66%..67%..68%..70%.. 71%..73%..74%..76%..77%..79%..80%.. 81%..83%..84%..86%..87%..89%..90%.. 91%..93%..94%..96%..97%..99%..done. using default bp penalty: 200 using default bp estimate min score: 386592 Starting with 620 multi-matches Computing genome content distance matrix... Genome conservation distance matrix: 0 0.579203 0.579203 0 Writing guide tree to C:\Users\c.valat\Desktop\reordering\alignment1\alignment1.guide_tree Exited with error code: -1073741819 What are your suggestions to resolve this problem. I thank you in advance for your answer. Best regards, Charlotte Valat Dr. Charlotte VALAT Chargé de projets scientifiques Anses - Laboratoire de Lyon Unité Antibioresistance et Virulence Bacteriennes (AVB) 31, avenue Tony Garnier 69364 LYON Cedex 07 Tel: 04 81 92 19 03 cha...@an...<mailto:den...@an...> [cid:image001.jpg@01D060BB.3AF41550] |
From: Aaron D. <aar...@uc...> - 2009-11-12 19:49:33
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Hello Mauve users: The Mauve development team is pleased to announce the official release of Mauve version 2.3.1. The new version of Mauve contains fixes for several bugs in the previous version, including better handling of mixed case characters and gaps in the SNP export, fixes to formatting of exported ortholog alignments, support for Windows 7 and versions of Mac OS X ranging from 10.3 to 10.6, and several other improvements. More details can be found on the Mauve version history web page. The new release can be downloaded from http://gel.ahabs.wisc.edu/mauve/download.php The change log is available from: http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-version-history.html |
From: Aaron D. <aar...@uc...> - 2009-06-17 17:23:10
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Dear Mauve users: The Mauve development team announces the immediate availability of version 2.3.0 of the Mauve genome alignment software. Mauve 2.3.0 contains major new functionality in the form of a contig reordering module for draft genomes. A manuscript by Rissman et al describing the contig reordering is in press at Bioinformatics. Also new in Mauve 2.3.0 are other often-requested features, including the ability to export lists and alignments of positionally orthologous genes, tRNAs, rRNAs and other annotated items; the ability to export lists of polymorphic sites; and other new features. Importantly, this release also fixes two critical bugs in the previous version that prevented computation and viewing of alignments made by progressiveMauve. We hope that you now find Mauve more stable and usable. Mauve 2.3.0 can be downloaded from http://gel.ahabs.wisc.edu/mauve/download.php A more complete list of changes is available from http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-version-history.html The manuscript describing reordering of draft genome contigs is available from: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp356 Kind regards, Aaron Darling, Ph.D. |
From: Aaron D. <da...@cs...> - 2008-06-24 13:42:50
|
Hello Mauve users: You are receiving this message because you elected to register your e-mail address when downloading the Mauve Genome Alignment Software. The Mauve development team announces the immediate release of Mauve 2.2.0. This new release focuses primarily on aligner bugfixes and accuracy improvement, and will provide the greatest benefit to people aligning large numbers of genomes and heavily rearranged genomes. The 2.2.0 release of progressiveMauve also has improved scalability over previous releases. progressiveMauve can now align drosophila genomes and when properly configured, mauveAligner can align mammalian genomes. To help get new features in the hands of users sooner, we have also initiated an automated build system. The build system takes a snapshot of the current aligner source code twice a week and compiles it. Such snapshots may be useful when a feature or bugfix has been implemented but not yet released. The snapshot site is linked from the bottom of the download page. Mauve 2.2.0 can be downloaded from: http://gel.ahabs.wisc.edu/mauve/download.php A more complete list of bugfixes is available from: http://asap.ahabs.wisc.edu/mauve/mauve-user-guide/ Source code is available from: http://gel.ahabs.wisc.edu/mauve/source/ Regards, Aaron Darling |
From: Aaron D. <da...@cs...> - 2007-11-27 09:11:08
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Hello Mauve Users, Mauve 2.1.1 has been released. Mauve 2.1.1 is an important bug fix release which addresses several troublesome issues present in last week's 2.1.0 release. Specifically the new release addresses problems on Mac OS X whereby it was not possible to construct genome alignments due to a missing "libgomp" image. Other problem issues that have been fixed include excessive memory usage in some cases, failure of the sequence navigator to highlight annotation search results, and an arithmetic bug that would on rare occasion cause a crash during progressiveMauve alignment anchor scoring. The new version can be downloaded from: http://gel.ahabs.wisc.edu/mauve/download.php Thanks go to those who gave quick feedback on the previous release! Regards, -Aaron You have received this e-mail because you (or somebody with your e-mail address) have registered for the Mauve mailing list when downloading Mauve. See the following page for unsubscribe information: https://lists.sourceforge.net/lists/listinfo/mauve-announce |
From: Aaron D. <da...@cs...> - 2007-11-20 14:26:32
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G'day Mauve users, After a long wait, the Mauve development team happily announces the birth of Mauve version 2.1.0. As usual, we have incorporated many new features and fixed several bugs that crept into the previous release. Importantly, this release includes 64-bit, parallel versions of the alignment algorithms which can take advantage of the fancy new Intel Core 2 and AMD processors in computers like the Mac Pro. Alignment parameters for Progressive Mauve have been further tuned for bacterial genomes in an effort to reduce erroneous alignments. Progressive Mauve now usually generates accurate alignments "out-of-the-box" without manual tuning of the minimum LCB weight parameter as required by the original Mauve algorithm. We have also made a substantial effort to rewrite the Mauve user guide to include information on Progressive Mauve and other developments made in the years since the User's guide was last updated. The new Mauve can be downloaded from: http://gel.ahabs.wisc.edu/mauve/download.php A more complete list of new features and bugfixes is available from: http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-version-history.html The new Mauve User's Guide is online at: http://asap.ahabs.wisc.edu/mauve/mauve-user-guide/ And in a printable PDF from: http://asap.ahabs.wisc.edu/mauve/downloads/UserGuide_latest.pdf Please direct any support questions to the mau...@li... mailing list, and report new bugs to the mailing list or the sourceforge.net bug tracker: http://sourceforge.net/tracker/?group_id=181544&atid=897627 Thanks for your continued support and feedback! Aaron Darling (on behalf of Mauve developers worldwide) You have received this e-mail because you (or somebody with your e-mail address) have registered for the Mauve mailing list. |
From: Aaron D. <da...@cs...> - 2007-01-29 07:54:30
|
This is a long e-mail. You are receiving it because your address was registered on the Mauve genome alignment web site. The major topics of this message are: (1) Mauve 2.0 officially released - easy accurate alignments! (2) New mailing list structure (3) Mauve development has moved to sourceforge.net Mauve 2.0 officially released -=-=-=-=-=-=-=-=-=-=- Mauve 2.0 includes an accurate new genome alignment algorithm called Progressive Mauve. The progressive alignment algorithm has been described in Aaron Darling's Ph.D. thesis, available from http://gel.ahabs.wisc.edu/~darling/darling_thesis.pdf Progressive Mauve features: * Substantially improved sensitivity on divergent genomes. Progressive Mauve can "climb a phylogenetic ladder" such that a pair of genomes with more than 1 substitution per site can be aligned if phylogenetic intermediate genomes are included in the alignment * Segments that are present in subsets of the genomes will be aligned. The original Mauve aligned only segments conserved in all genomes. * A configurable substitution matrix dictates the LCB and alignment scores. The substitution matrix gives Mauve additional power in distinguishing true homology from random sequence similarity. In the original algorithm LCBs were scored based on the sum of multi-MUM lengths * A random-walk homology test identifies conserved "backbone" segments. Random walk statistics similar to those used in Gapped-BLAST are used to identify pairwise conserved segments. Pairwise homologies are then combined by transitive homology relationships to identify segments conserved in two or more genomes. * Progressive Mauve can scale to hundreds of genomes. We have successfully aligned over a hundred poxvirus genomes, hundreds of Hepatitis C Virus genomes, and the genomes of over thirty enterobacteria. A substantial amount of computer memory is required for large alignments. Anna Rissman has contributed a new annotation search interface that tremendously improves browsing genomes with annotated sequence features. The new search interface can: * Jump directly to a particular numerical coordinate in a particular genome * Jump directly to an annotated feature of a particular name * Search for and list annotated features by any part of their name or qualifying value. Searchable fields include things like CDS name, product description, GO terms, database x-refs, and amino acid subsequences Additional new features and bugfixes are described on the Mauve version history web page: http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-version-history.html New mailing list structure -=-=-=-=-=-=-=-=-=-=- Previously, Mauve related announcements were made via the gel-software mailing list. That mailing list is now defunct and we have migrated to sourceforge.net mailing lists. Two sf.net mailing lists have been created: mauve-announce and mauve-users. The mauve-announce mailing list is a low-traffic list intended for software release announcements. To ensure the list stays low-traffic, only Mauve developers can post to mauve-announce. The mauve-users list, on the other hand, provides a general discussion forum for Mauve users to share experiences, praise, and complaints about the software. Any registered Mauve user can post to this list and the list is moderated to prevent spam. Archives of mailing list traffic will become available at this page: http://sourceforge.net/mail/?group_id=181544 and will also be indexed by google and mail-archive.com. Mauve development has moved to sourceforge.net -=-=-=-=-=-=-=-=-=-=- We have transitioned Mauve's source code repository to the sourceforge.net site, and the complete source code is available via subversion. We hope that moving the project to sourceforge will make Mauve development more transparent and accessible to other software developers. More importantly, sourceforge provides a bug and feature tracking service that we encourage people to use, available at web page: http://sourceforge.net/tracker/?group_id=181544&atid=897627 The bug tracker allows one to report new bugs and check the status of known bugs in the Mauve software. Our previous bug tracking software suffered a series of security failures and had to be removed... Other news -=-=-=-=-=-=-=-=-=-=- The structure of the Mauve web site has changed. Please update any links and bookmarks. Anna Rissman has joined the dev team, welcome! And thanks go to... Bob Mau for patient testing of Mauve 2.0 Nicole Perna and the Genome Evolution Lab for supporting this project Eduardo Rocha for valuable suggestions about alignment scoring Everybody else who offered time and suggestions! |