http://trimal.cgenomics.org/ 2010-09-10T11:34:13+02:00 http://trimal.cgenomics.org/ http://trimal.cgenomics.org/lib/images/favicon.ico text/html 2009-04-20T09:16:03+02:00 http://trimal.cgenomics.org/changelog?rev=1240211763&do=diff * Added the htmlout to track the trimAl's trimming. * Added the possibility to delete spurious sequences from the alignment. * Added the complementary and colnumbering options. * Added the manual selection of columns. * Added one new heuristic method to select the best automated trimming method. * Automated1 text/html 2010-06-24T22:39:11+02:00 http://trimal.cgenomics.org/downloads?rev=1277411951&do=diff trimAl v1.3 is our current under development version. You can find the official repository here: <http://github.com/scapella/trimal>. We expect to release the next official version trimAl v.1.4 during summer of 2010. If you have any suggestion or idea, don't hesitate to contact us. You can subscribe to our mailing list to get the latest news. text/html 2009-06-11T09:23:54+02:00 http://trimal.cgenomics.org/faq?rev=1244705034&do=diff * What similarity matrices does trimAl use? * trimAl uses, by default, the BLOSUM62 similarity matrix in proteins and the Identity matrix in DNA/RNA sequence alignments. However, the users can upload any other matrix of their choice (see below) text/html 2009-07-21T11:01:50+02:00 http://trimal.cgenomics.org/getting_started_with_trimal_v1.2?rev=1248166910&do=diff Thank you for choosing trimAl v1.2 to trim your alignments. In this version we have solved some bugs from the previous version and we have also added new functionality to the program. You will see that it is very easy to get familiar with the program. The first thing you need to do to start is to decide whether you will be using trimAl in its command line version or through the web interface. The command line version is faster and has more possibilities, so it is recommended if you are going to … text/html 2009-04-29T10:59:50+02:00 http://trimal.cgenomics.org/introduction?rev=1240995590&do=diff Multiple sequence alignments (MSA) are central to many areas of bioinformatics and evolutionary biology. They are not only used in the phylogenetic analyses of biological sequences but also in many other bioinformatics applications such as homology modeling, database searchers and motif finding. Recently, such multiple sequence alignment based techniques have been incorporated in high-throughput pipelines such as genome annotation and large-scale phylogenetics. In all these applications the reli… text/html 2010-05-06T18:53:21+02:00 http://trimal.cgenomics.org/mailing_list?rev=1273164801&do=diff If you want to be informed about important news such as new releases, publications, etc, please, subscribe using your personal information in the form below. text/html 2009-09-15T12:28:44+02:00 http://trimal.cgenomics.org/news?rev=1253010524&do=diff * June 08, 2009. A paper describing trimAl v1.2 has been published in Bioinformatics you can access the paper * June 01, 2009. trimAl has been accepted by Bioinformatics. * April 28, 2009. The final revision of trimAl v1.2 is released. * April 11, 2009. trimAl v1.2 is released. text/html 2009-04-19T18:18:06+02:00 http://trimal.cgenomics.org/older_versions?rev=1240157886&do=diff In this section you can find the previous versions of trimAl and, in the future, readAl. * Getting started with trimAl v1.1 * trimAl v1.1 command line version * trimAl v1.1 webserver interface text/html 2009-09-16T12:38:19+02:00 http://trimal.cgenomics.org/publications?rev=1253097499&do=diff If you use trimAl, please cite: [trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses]. Salvador Capella-Gutierrez; Jose M. Silla-Martinez; Toni Gabaldon. Bioinformatics 2009 25: 1972-1973. Supplementary information: text/html 2010-09-09T15:30:09+02:00 http://trimal.cgenomics.org/sidebar?rev=1284039009&do=diff [] OVERVIEW * Introduction * Publications * News * trimAl team * FAQ * Mailing list DOCUMENTATION * Getting started with trimAl v1.2 * Use of the trimAl v1.2 command line * Use of the trimAl v1.2 webserver interface * Getting started with readAl v1.2 text/html 2009-06-10T10:42:01+02:00 http://trimal.cgenomics.org/trimal?rev=1244623321&do=diff This is trimAl's information page. Also, you can find information related to the readAl program. trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment Access trimAl publication text/html 2009-06-11T09:22:15+02:00 http://trimal.cgenomics.org/trimal_team?rev=1244704935&do=diff * Salvador Capella-Gutiérrez [scapella _at_ crg.es] * Toni Gabaldón [tgabaldon _at_ crg.es] * Jose M. Silla-Martínez (trimAl v1.1). text/html 2009-04-19T17:48:15+02:00 http://trimal.cgenomics.org/use_of_the_command_line_trimal_v1.2?rev=1240156095&do=diff Basic usage trimal -in <inputfile> -out <outputfile> -(other options) Common options -h Print this information and show some examples. --version Print the trimAl version. -in <inputfile> Input file in several formats (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip). -compareset <inputfile> Input list of paths for the files containing the alignments to compare. -matrix <inpufile> Input file for user-defined similar… text/html 2009-04-19T20:25:12+02:00 http://trimal.cgenomics.org/use_of_the_readal_v1.2?rev=1240165512&do=diff Thank you for choosing readAl v1.2 to convert your alignments. You will see that it is very easy to get familiar with the program. The first thing you need to do to start is decide whether you will be using readAl in its command line version or through the web interface. text/html 2009-04-19T20:23:45+02:00 http://trimal.cgenomics.org/use_of_the_trimal_v1.2_webserver_interface?rev=1240165425&do=diff trimAl v1.2 has been implemented in the new Phylemon webserver version, an online platform for phylogenetic and evolutionary analyses of molecular sequence data. The trimAl webserver included in Phylemon provides a user friendly interface and the opportunity to concatenate your trimmed alignment to many different phylogenetic analyzes.