selectome.unil.ch
Selectome: a database of Positive SelectionSelectome is a database of positive selection - based on a rigorous branch-site likelihood test - detected using CODEML on all branches of gene trees
http://selectome.unil.ch/
Selectome is a database of positive selection - based on a rigorous branch-site likelihood test - detected using CODEML on all branches of gene trees
http://selectome.unil.ch/
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Selectome: a database of Positive Selection | selectome.unil.ch Reviews
https://selectome.unil.ch
Selectome is a database of positive selection - based on a rigorous branch-site likelihood test - detected using CODEML on all branches of gene trees
selectome.unil.ch
References - Selectome
http://selectome.unil.ch/cgi-bin/cite.cgi
Selectome: a Database of Positive Selection. Selectome update: quality control and computational improvements to a database of positive selection. Sébastien Moretti, Balazs Laurenczy, Walid H. Gharib, Briséïs Castella, Arnold Kuzniar, Hannes Schabauer, Romain A. Studer, Mario Valle, Nicolas Salamin, Heinz Stockinger, Marc Robinson-Rechavi. Selectome: a Database of Positive Selection. Romain A. Studer. Patterns of Positive Selection in Seven Ant Genomes. Studies in Health Technology and Informatics. Phylo...
Downloads - Selectome
http://selectome.unil.ch/cgi-bin/download.cgi
Selectome: a Database of Positive Selection. Runs faster with OpenBLAS than with BLAS). Multiple Sequence Alignments and Trees, Selectome v06. Based on Ensembl 68, Euteleostomi. Sub-taxa, on Ensembl 70, Primates. Sub-taxa, on Ensembl 71, Glires. Sub-taxa, and on Ensembl Genomes 71-18, Drosophila. Based on Ensembl 61, Primate. Based on TreeFam 7, A and B families and Euteleostomi. Based on TreeFam 7, A families and Euteleostomi. Based on TreeFam 6, A families and Euteleostomi.
News - Selectome
http://selectome.unil.ch/cgi-bin/news.cgi
Selectome: a Database of Positive Selection.
Guide/Howto - Selectome
http://selectome.unil.ch/cgi-bin/guide.cgi
Selectome: a Database of Positive Selection. You can use the left box to do a basic search. Basic search accepts diverse entries, including Ensembl. Gene and gene tree identifiers, gene, transcript or protein names, Uniprot. Protein names or accession numbers, cross-references (Gene Ontology, InterPro, .), or keywords. You can use the '. Menu to restrict your search to a specific data type and also to search lists of Ensembl or Cross-References IDs. You can also use the '. And by gene family. Family/Tree...
Methods - Selectome
http://selectome.unil.ch/cgi-bin/methods.cgi
Selectome: a Database of Positive Selection. CodeML is a program from the package PAML. It estimates various parameters (Ts/Tv, dN/dS, branch length) on the codon (nucleotide) alignment, according to the phylogenetic tree. The parameter of interest to us is ω = dN/dS. Which indicates selective pressure. Selectome uses the branch-site model. Which estimates different dN/dS values among branches and among sites. A branch of interest is selected and called ". 34; All other branches in the tree are the ".
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nigel delaney | evolutionary biologist, statistician, nice guy
http://evolvedmicrobe.com/blogs
Evolutionary biologist, statistician, nice guy. C# vs Java, Xamarin vs. Oracle, Performance Comparison version 2.0. Today I noticed the SIMD implementation of the Mandelbrot set algorithm I blogged about last year was successfully submitted to the language shootout webpage. However, I was a bit disappointed to see the C# version was still slower than the Java version, despite my use of the special SIMD instructions (though I was pleased that a quick port of my code to F#. C# may use a lot less memory, bu...
jalview.org
http://www.jalview.org/community/links
Skip to main content. Jalview and JABA Slides. Jalview and JABA Slides. Jalview has been used for several years on many websites as a visualization tool for database search results or alignment algorithms, as well as being part of several training courses. The following links are to projects which are actively using new features in Jalview version 2 . If you would like to add your project to the list, send a message to the usual address. BMC Bioinformatics. [ PubMed. MAFFT is a program for the multiple a...
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Selectome: a database of Positive Selection
Selectome: a Database of Positive Selection. Selectome is a database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML. On all branches of animal gene trees. The web interface of Selectome enables queries according both to the results of positive selection tests, and to gene related criteria. Test results including positively selected sites can be visualized on the tree, and on the protein sequence alignment.
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