Enlaces

a sitios web de interés

Introducciones

A step by step guide to phylogeny reconstruction. C. Jill Harrison and Jane A. Langdale. The Plant Journal, Vol. 45: 561. 2006. (PDF).

Bases para Taxonomia e Sistemática. Enlaces, lista de referencias. Silvio Nihei, Sao Paulo, Brasil.

Bioinformática: de las secuencias a la genómica comparada. (PDF). Articulo de difusión en la revista Ciencia y Desarrollo. México.

La búsqueda del Método Natural. Libro. Autor: Jorge Llorente B. (Sitio web con acceso a los capítulos del libro)

Cladistica. Contribución en Wikipedia, la enciclopedia libre.

Métodos de análisis en la reconstrucción filogenética. "Breve estudio critico de los tres principales métodos taxonómicos: fenético, cladista y la sistemática ortodoxa o evolutiva.... Breve exposición de la metodología de reconstrucción filogenética". Emilio J. López Caballero y Gonzalo Pérez Suárez. Bol. S.E.A., nº 26, 1999 : 45-56.

Sistemática Biológica: avances y direcciones en la teoría y los métodos de la reconstrucción filogenética. Revisión publicada en la revista Hidrobiológica 15(3): 351-370. E. De Luna, E., JA. Guerrero & T. Chew-Taracena. 2005.

Tree-thinking. "This site is designed to be a resource for teachers, students, and researchers who are interested in tree thinking. It contains materials for teaching and learning about evolutionary relationships and the use of phylogenies in biological problem solving". 

What, if anything, is a Zebra. The essay (and reading guide) addresses the issue of cladistics, and some of the problems encountered in the science of Systematics.

Conceptos y Métodos

Journey into Phylogenetic Systematics. Sitio de la Universidad de Berkeley con introducción de los métodos cladísticos.

Phylocode. "The PhyloCode is a formal set of rules governing phylogenetic nomenclature. It is designed to name the parts of the tree of life by explicit reference to phylogeny".

Phylogenetics: just methods. "This site is designed to .... provide you with an understanding of the various methods you might encounter so as to allow you to make informed decisions about what you think is defensible and appropriate" Mark E. Siddall.

Phylogeny and Reconstructing Phylogenetic Trees. "These few pages describe the problem of reconstructing phylogenetic trees with the help of a Java applet. I wrote the applet to discover more about the java language and the API interface. I've been interested in phylogenetic trees for some time and thought they would make a good subject. -- Dave Joyce"

Glosarios

Introductory Glossary of Cladistic Terms. Michael D. Crisp, Australian National University. Glosario básico.

Glosario. Instituto Nacional de Ecología. México.

Software

Bioinformatics.org. "The Bioinformatics Organization, Inc. serves the scientific and educational needs of bioinformatic practitioners and the general public. We develop and maintain computational resources to facilitate world-wide communications and collaborations between people of all educational and professional levels. We provide and promote open access to the materials and methods required for, and derived from, research, development and education".

Bio::NEXUS. An object-oriented NEXUS applications programming interface (API) in Perl, along with two demonstration applications, nexplot  and nextool (a scriptable editor). Arlin Stoltzfus.

Bio-Phylo. Phylogenetic analysis using Perl. Rutger Vos.

Bosque. "Phylogenetic Trees Drawing Tool. Bosque (means forest in spanish) is a free graphical tool that allows easily to draw, manipulate and prints phylogenetic trees in the Newick format, which is the typical output format from phylogenetic programs, such as the ones present on the Phylip package". Bosque has been developed by Salvador Ramirez at PROFC - Universidad de Concepción.

CAFCA. A Collection of APL Functions for Cladistic Analysis. CAFCA employs the methods of group-compatibility and component-compatibility to run a cladistic analysis of a data matrix.

Cladistics.com. Sitio con enlaces para los programas de Winclada, NONA, TNT y Trees.

HyPhy. HYPHY (pronounced as Hi-fi) is an abbreviation for [Hy]Pothesis Testing Using [Phy]logenies. It is a free multiplatform (Mac, Windows and UNIX) software package intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses. Sergei L. Kosakovsky Pond.

Mesquite. "Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed".

MorphoBank. "The database catalogues images (including films and CT scans) submitted by scientists. For phylogenetic research, MorphoBank displays dynamic phylogenetic matrices of morphological characters with labeled homology statements. MorphoBank facilitates virtual collaboration by teams of researchers, especially those building phylogenetic matrices with affiliated image data".

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. This includes a wide range of tools from the most basic for multiple sequence alignment to elaborate statistical methods of phylogenetic reconstruction including methods for evolutionary rates analyses and molecular adaptation. The server is freely accessible in the internet at phylemon , and it is described in: Tarraga J, Medina I, Arbiza L, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H. Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics..Nucleic Acids Res 2007 (Web server issue).

PhyloFacts. "The Berkeley Phylogenomics Group presents PhyloFacts, a structural phylogenomic encyclopedia containing almost 10,000 'books' for protein families and domains, with pre-calculated structural, functional and evolutionary analyses. PhyloFacts enables biologists to avoid the systematic errors associated with function prediction by homology through the integration of a variety of experimental data and bioinformatics methods in an evolutionary framework. Users can submit sequences for classification to families and functional subfamilies".

Phylogeny Programs. (Joe Felsenstein, University of Washington). Sitio donde se pueden encontrar la mayoría del software para análisis filogenético.

PhyloPat. "Phylogenetic Pattern Analysis of eukariotic genes. PhyloPat uses the latest release of EnsMart (release 41), and their one-to-one, one-to-many and many-to-many orthologies".

POY (Phylogenetic Analysis of DNA and other data using Dynamic Homology). Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2007. POY 4.0 Beta 1665.

PRAP. Calcula soporte de Bremer en ambiente Windows, Macintosh y Linus.

SplitsTree4. "SplitsTree4 is the leading application for computing evolutionary networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks."

Taxonomic Search Engine. "Federating taxonomic databases using web services".

TNT. Tree analysis using New Technology. A new program by Pablo Goloboff, Steve Farris, and Kevin Nixon.

TreeBASE. A relational database of phylogenetic information. TreeBASE stores phylogenetic trees and the data matrices used to generate them from published research papers. William H. Piel.

tREeBOOT. A Java program (with methods described in Moore et al. 2006) to perform a variety of supertree bootstrapping analyses, in conjunction with paup and mincut (Page). Stephen A. Smith.

Tree View. "TreeView X is an open source program to display phylogenetic trees on Linux, Unix, Mac OS X, and Windows platforms. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). The program was written by Rod Page."

Listas de referencias, Bibliotecas Virtuales y Revistas en línea

Biological Theory. Biological Theory: Integrating Development, Evolution, and Cognition is devoted to theoretical advances in the biological and cognitive sciences. Its emphasis is on the conceptual integration afforded by evolutionary and developmental approaches. {contribuido por Dr. Francisco Vergara}

BMC Bioinformatics. "BMC Bioinformatics is an open access journal publishing original peer-reviewed research articles in all aspects of computational methods used in the analysis and annotation of sequences and structures, as well as all other areas of computational biology".

BMC Evolutionary Biology. "BMC Evolutionary Biology is an open access journal publishing original peer-reviewed research articles in all aspects of molecular and non-molecular evolution of all organisms, as well as phylogenetics and palaeontology".

BMC Frontiers in Zoology. "Frontiers in Zoology is an Open Access, peer-reviewed, online journal publishing high quality research articles and reviews on all aspects of animal life".

CiteULike. "CiteULike is a free service to help academics to share, store, and organise the academic papers they are reading. When you see a paper on the web that interests you, you can click one button and have it added to your personal library".

Evolutionary Bioinformatics OnLine. "Evolutionary Bioinformatics Online is an international, peer-reviewed journal focusing on evolutionary bioinformatics. .... Evolutionary Bioinformatics Online publishes papers on all aspects of computational evolutionary biology, and evolutionary bioinformatics.

eVolución. Boletín electrónico de la Soc. Española de Biología Evolutiva. {contribuido por Claudia Hornung}

HighWire Press. "A division of the Stanford University Libraries, HighWire Press hosts the largest repository of high impact, peer-reviewed content, with 999 journals and 3,801,164 full text articles from over 130 scholarly publishers. HighWire-hosted publishers have collectively made 1,478,214 articles free. With our partner publishers we produce 71 of the 200 most-frequently-cited journals".

Latindex. "Latindex es producto de la cooperación de una red de instituciones que funcionan de manera coordinada para reunir y diseminar información bibliográfica sobre las publicaciones científicas seriadas producidas en la región".

Phylogenetics. List of publications. Wikipedia.

Phylogenetic Inferencing: Beyond Biology. "Journal of Biomedical Informatics, 2006; Volume 39, Issue 1 (free). A special journal issue dedicated almost entirely to review articles about contemporary phylogenetic methods". Acceso gratis a los nueve artículos en PDF. Al entrar a la página de la revista, seleccione en la caja de la izquierda el enlace "Volume 39, Issue 1"

Phyloinformatics. "A peer reviewed, free and open access journal dedicated to publishing high quality papers on the use of informatics in taxonomy".

Phylogenetics and Self-Organization in Ecology. Workshop 1 Phylogeography and Phylogenetics (September 26-30, 2005). Organizers: Craig Moritz, Michael Hickerson, and Dennis Pearl. Current Topics Workshop – The Problems of Phylogenetic Analysis of Large Datasets (December 1-2, 2005). Organizers: Daniel Janies, Diego Pol, John Wenzel, Dennis Pearl, and Ward Wheeler.

The Phylofiles. "The Phylogenetics Resource Site. Our aim is to create a comprehensive resource for Phylogenetics on the internet."

PLOS. Computational Biology. "PLoS Computational Biology features works of exceptional significance that further our understanding of living systems at all scales through the application of computational methods".

Reading lists. Referencias para el curso "Principles of Phylogenetics: Systematics", UC Berkeley.

RedAlyc. La hemeroteca científica en línea. "Red de Revistas Científicas de America Latina y el Caribe, España y Portugal".

ReviCien. "La Red de Revistas Científicas Españolas reúne a las principales publicaciones científicas editadas en España. Esto convierte a la plataforma en un valioso recurso online para investigadores, estudiantes y bibliotecas".

Revista Mexicana de Biodiversidad. Sitio con enlaces a los artículos en PDF.

Reports. Board on Life Sciences. Biodiversity. Sitio de la National Academy of Sciences, con enlaces a libros en html o PDF.

SciElo. "The Scientific Electronic Library Online - SciELO is an electronic library covering a selected collection of Brazilian scientific journals".

SuperTree Bibliography. By James Cotton & Joe Thorley.

Taxonomy for the Twenty-first century. Philosophical Transactions of the Royal Society B: Biological Sciences 359, #1444. 2004. Número especial con 19 artículos disponibles en línea.

Trees of History Bibliography. "Trees of History in Systematics, Historical Linguistics, and Stemmatics: A Working Interdisciplinary Bibliography Version of March 1993. This bibliography was compiled by Robert J. O’Hara".

Workshop on Molecular Evolution. Lista extensa de referencias. Muchas de ellas disponibles en PDF ahi mismo.

Sociedades

Red Colombiana de Biologia Evolutiva

The Systematics Association.

SEBA. Systematic and Evolutionary Biogeographical Association.

SESBE. Sociedad Española de Biología Evolutiva. {contribuido por Claudia Hornung}

Society of Systematic Biologists.

Willi Hennig Society.

Interés general

La Biodiversidad de México. "Sitio electrónico del Segundo Estudio de País (2EP). Quienes participamos en el 2EP nos proponemos que éste sea la fuente más completa de información (primaria, compilada, descriptiva, sintetizada, analizada y actualizada) sobre el estado (tendencias, respuestas y escenarios futuros) del conocimiento de la diversidad biológica de México, su conservación y pérdida, su uso sustentable y su relación con el bienestar humano". CONABIO.

Bioinformatica.info. "Bioinformatica.info es un portal de noticias y recursos hecho por Genes Digitales".

Biología Comparada en Latinoamérica. Articulo (disponible en pdf). Juan Jacobo Schmitter Soto. Ecosur. México.

Biologia Evolutiva, Filogenética, Sistemática, Taxonomía. Colección de enlaces del sitio web del Instituto de Ecología, UNAM.

BiologyBrowser.  "BiologyBrowser, produced by Thomson Scientific, is a free web site offering resources for the life sciences information community".

CIPRES: Building the Tree of Life: A National Resource for Phyloinformatics and Computational Phylogenetics. The goal of the CIPRES project is to enable large-scale phylogenetic reconstructions on a scale that will enable analyses of huge datasets containing hundreds of thousands of bio molecular sequences.

La Filogenia frente a la justicia. Articulo en la revista Ciencia Hoy. Jorge V. Crisci y Liliana Katinas Museo de La Plata. Argentina.

La Filogenia del lenguaje. "Un método biológico aplicado a la gramática descubre vínculos entre lenguas antiguas". Noticia en La Flecha. Diario de ciencia y tecnología. 7 Oct 2005.

Filosofía e Historia de la Biología. Facultad de Ciencias UNAM.

MORPH. "A Research Coordination Network supported by the National Science Foundation to promote a modern synthesis in plant evolutionary developmental biology".

National Evolutionary Synthesis Center. "Our goal is to help foster a grand synthesis of the biological disciplines through the unifying principle of descent with modification".

NSF: Partnerships for Enhancing Expertise in Taxonomy (PEET). "In partnership with academic institutions, botanical gardens, freshwater and marine institutes, and natural history museums, the National Science Foundation seeks to enhance taxonomic research and help prepare future generations of experts".

Phylodiversity network.  The evolutionary component of biodiversity. "A permanent home for biodiversity, systematics, phylogenetics, and bioinformatics research".

PhyloSphere. This phylofeed aggregates content from several websites in the phylogenetic cyberspace! You too can share links to articles or photos! Join the PhyloSphere.

La sistemática en México. Articulo publicado  en la revista de divulgación ELEMENTOS, de la Universidad de Puebla. México. (disponible en pdf)

Sistemática en el INECOL. Blog sobre la investigación, cursos de posgrado y foro de discusión de los investigadores, técnicos y estudiantes del área de Sistemática del Instituto de Ecología AC, Xalapa, México.

Tree of Life. "The Tree of Life Web Project (ToL) is a collaborative effort of biologists from around the world. On more than 4000 World Wide Web pages, the project provides information about the diversity of organisms on Earth, their evolutionary history (phylogeny), and characteristics".

Yahoo!: Evolution > Phylogeny. Site listings.

Who is who in Phylogenetic Networks: Articles, Authors and Programs. By Philippe Gambette.

Grupos de discusión

 

Comentarios. Publique sus opiniones y lea los comentarios sobre el sitio web filogenetica.org en el blogger "filogenetica"

Clado-l. Lista Venezolana de discusión en Cladistica. "Esta lista de correos proporciona a los suscriptores la posibilidad de solicitar información sobre aspectos relacionados con la sistemática filogenética y el método cladístico. Igualmente permite la discusión abierta de problemas particulares con respectos a análisis cladísticos en proceso o como iniciar éstos".

Foro de Mesquite.

Fórum de Sistemática e Evolução. "O Fórum visa estimular discussões de tópicos amplos relacionados à Sistemática e Evolução biológica, promovendo o desenvolvimento do pensamento teórico e da interação entre estas áreas e outras subdisciplinas biológicas".

iPhylo. "Phyloinformatics Blog".

Systematics and Biogeography. "Systematics & Biogeography is the Companion Blog to the book Foundations of Systematics and Biogeography. The blog hopes to discuss concepts in the book as well as ideas and current events that affect taxonomy, systematics and biogeography. Foundations of Systematics and Biogeography by D.M Williams & M.C. Ebach is published by Springer and is available from Amazon.com"

Yahoo! Argentina, Grupo de discusión. "Descripción: Para pensar y discutir sobre teoría y práctica de cladística". {contribuido por Dr. Martín Ramírez, Argentina}

Yahoo! Brasil, Grupo de discusión. "Descrição: Este grupo possui o intuito de permitir a troca de informação entre pesquisadores e estudantes a respeito da metodologia cladística em todos os seus aspectos. Discussão de métodos e experiências".

WebLog de Bioinformática. Bienvenid@ al primer weblog de Bioinformática en España. Este blog ha sido creado como un punto de encuentro y discusión de la comunidad bioinformática de nuestro ámbito más cercano.

 

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