Explore your sequence alignments for evidence of adaptive or purifying evolution, build NJ trees and select appropriate evolutionary models using fast likelihood based methods on our server..
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Adaptive Evolution Server @ Datamonkey.org | datamonkey.org Reviews
https://datamonkey.org
Explore your sequence alignments for evidence of adaptive or purifying evolution, build NJ trees and select appropriate evolutionary models using fast likelihood based methods on our server..
Datamonkey Adaptive Evolution Server
Looking for something more familiar? Click here for Datamonkey Classic. Datamonkey is funded jointly by MIDAS. And NIH award R01 GM093939.
datamonkey.org
Adaptive Evolution Server @ Datamonkey.org
http://www.datamonkey.org/dataupload_scueal.php
SCUEAL data upload page. Choose an HIV sequence file with sequences to subtype with the SCUEAL. Algorithm. The sequences do not have to be aligned. data formats. Currently only POL sequences can be subtyped. UCSD Viral Evolution Group 2004-2017.
A brief overview of DEPS
http://www.datamonkey.org/help/deps.php
How does DEPS infer directional selection? Complete method details can be found in our Molecular Biology and Evolution. UCSD Viral Evolution Group 2004-2017.
A brief overview of Branch-site REL
http://www.datamonkey.org/help/bsr.php
How does Branch-Site REL infer episodic diversifying selection? Branch-site REL will perform a series of LRT tests to identify all lineages in a phylogeny where a proportion of sites evolves with dN/dS 1, i.e. instances of episodic (dN/dS varies across the tree) diversifying selection at a proportion of sites (dN/dS varies across sites). As such, this model is a generalization of existing branch-site methods. UCSD Viral Evolution Group 2004-2017.
Help on using Spidermonkey to detect co-evolving sites
http://www.datamonkey.org/help/spidermonkey.php
How does Spidermonkey work? Our application note on Spidermonkey has been published online at Bioinformatics Advance Access. This method was introduced in the evolutionary context in our paper. On the evolution of the phenotypically important and highly variable V3 loop of the envelope glycoprotein in HIV-1. Spidermonkey is an analytical pipeline (series of data-processing algorithms) for identifying co-evolving sites. And amino acid sequences. Because Spidermonkey utilizes the same data input methods as...
A brief overview of Evolutionary Fingerprinting
http://www.datamonkey.org/help/esd.php
What is evolutionary fingerprinting? Complete method details can be found in this Molecular Biology and Evolution. UCSD Viral Evolution Group 2004-2017.
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El rincon natural: 4/10/09 - 11/10/09
http://elrinconatural.blogspot.com/2009_10_04_archive.html
Blog para discutir diversos temas en ciencia y sociedad. Natural Place. A blog to discuss about science and social topics. Y donde quedó la archeospora? Ardi al descubierto: Estreño mundial en Discovery . La visita de los nativos. Cómo poner imágenes con liga hacia otro sitio. Fossil rewrites early human evolution. Mandriva Vs Ubuntu, a word from a experienced user. Creation: the Movie. starring: Paul Betanny as cha. Estrenando. o Vel rosita? Se ha producido un error en este gadget. Ver todo mi perfil.
El rincon natural: 20/12/09 - 27/12/09
http://elrinconatural.blogspot.com/2009_12_20_archive.html
Blog para discutir diversos temas en ciencia y sociedad. Natural Place. A blog to discuss about science and social topics. Y donde quedó la archeospora? Feliz Navidad y Próspero Año Nuevo. Happy Holidays. Se ha producido un error en este gadget. Petri foot 18/8/16 - 1 via http:/ ift.tt/2bhA6F7 - Complete post @ http:/ ldalcaraz.blogspot.com This work is licensed under a Creative Commons Attribut. Laboratorio de Epigenética y Biología del Desarrollo de la Universidad Veracruzana. Ver todo mi perfil.
El rincon natural: 6/12/09 - 13/12/09
http://elrinconatural.blogspot.com/2009_12_06_archive.html
Blog para discutir diversos temas en ciencia y sociedad. Natural Place. A blog to discuss about science and social topics. Y donde quedó la archeospora? Google Chrome for linux. ahh, finally. Se ha producido un error en este gadget. Petri foot 18/8/16 - 1 via http:/ ift.tt/2bhA6F7 - Complete post @ http:/ ldalcaraz.blogspot.com This work is licensed under a Creative Commons Attribut. Laboratorio de Epigenética y Biología del Desarrollo de la Universidad Veracruzana. The journal of Feelsynapsis. I encour...
El rincon natural: 1/11/09 - 8/11/09
http://elrinconatural.blogspot.com/2009_11_01_archive.html
Blog para discutir diversos temas en ciencia y sociedad. Natural Place. A blog to discuss about science and social topics. Y donde quedó la archeospora? Se ha producido un error en este gadget. Petri foot 18/8/16 - 1 via http:/ ift.tt/2bhA6F7 - Complete post @ http:/ ldalcaraz.blogspot.com This work is licensed under a Creative Commons Attribut. Pues ya es 2015 (felicidades a quienes deseen recibir una felicitación por el cambio de año). Después de mucho tiempo sin publicar y en espera de que vario.
Evolutionary Genetics Software Links by Sergios-Orestis Kolokotronis
http://softlinks.amnh.org/molevol.html
Performs a multitude of tests and analyses, including coalescent simulations. Populations can be mouse-defined. A program package implementing a variety of sophisticated models of nucleotide and protein sequence evolution via ML. Allows to test alternative hypotheses using likelihood ratio tests. Not recommended for tree-building. Handy for ML and hypothesis testing. Also tests for selection. Customizable through its batch language. Simulates the evolution of nucleotide and aminoacid sequences along a ph...
El rincon natural: 30/05/10 - 6/06/10
http://elrinconatural.blogspot.com/2010_05_30_archive.html
Blog para discutir diversos temas en ciencia y sociedad. Natural Place. A blog to discuss about science and social topics. Y donde quedó la archeospora? Uff sólo el comienzo o ya por fin a terminar? Se ha producido un error en este gadget. Petri foot 18/8/16 - 1 via http:/ ift.tt/2bhA6F7 - Complete post @ http:/ ldalcaraz.blogspot.com This work is licensed under a Creative Commons Attribut. Laboratorio de Epigenética y Biología del Desarrollo de la Universidad Veracruzana. The journal of Feelsynapsis.
El rincon natural: 7/11/10 - 14/11/10
http://elrinconatural.blogspot.com/2010_11_07_archive.html
Blog para discutir diversos temas en ciencia y sociedad. Natural Place. A blog to discuss about science and social topics. Y donde quedó la archeospora? Deep ocean species discovered. Se ha producido un error en este gadget. Petri foot 18/8/16 - 1 via http:/ ift.tt/2bhA6F7 - Complete post @ http:/ ldalcaraz.blogspot.com This work is licensed under a Creative Commons Attribut. Laboratorio de Epigenética y Biología del Desarrollo de la Universidad Veracruzana. The journal of Feelsynapsis. Mass groupings o...
Hulab Journal Club: May 2010
http://hulabjournalclub.blogspot.com/2010_05_01_archive.html
News on selected scientific papers, including molecular evolution, systematics, floral evo-devo, reproductive biology in various botanical literatures. Thursday, May 27, 2010. Paper]Complex distribution patterns, ecology and coexistence of ploidy levels of Allium oleraceum (Alliaceae) in the Czech Republic. Martin Duchoslav, Lenka S ˇ afa´rˇova´. 出處: Annals of Botany, 2010, 105: 719-735. Letter] Genome streamlining in prokaryotes versus eukaryotes. 出處: Trends in Ecology and Evolution, 2010, 25(6), 320-321.
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Adaptive Evolution Server @ Datamonkey.org
A new method, BUSTED. A new approach to identifying gene-wide evidence of episodic positive selection where the non-synonymous substitution rate is transiently greater than the synonymous rate, is available for use here. A new tool, a Newick Tree Viewer. Is available to view, manipulate, and annotate Newick formatted trees from within your browser. A new method, RELAX. A general hypothesis testing framework for detecting relaxed selection in a codon-based phylogenetic framework, is available for use here.
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