LMs4TNT: Java tool to convert xy coordinates to a TNT data block

I am glad to make available a Java program that reads “x, y” coordinates of landmarks and semilandmarks from each specimen (tps or row format), estimates means for each group, and writes blocks of terminal names and the coordinates with the corresponding commands as required by TNT phylogenetic software.

You can download "jt4tnt.class" at the following URL:

http://www.filogenetica.org/Java_tool/lms4tnt.htm

Please note that “jt4tnt.class” is a java tool, thus it is platform independent. This program requires Java 6 or later (Java 1.6). Runs from your system command window writing a command line with several expressions separated by a space.

As an example, the following command line will read 300 configurations in a tps file “my300configs.tps”, will calculate means for 10 groups according to the labels in “membership10spp.txt”, and will write these in the output file “my10spp.txt” with all necessary TNT commands:

>java jt4tnt -i my300configs.tps -o my10spp.txt -m membership10spp.tx

There is more info on examples, input data file formats, membership list file, and output files in the website.

I guess you can cite this tool as:
Sandria, J. & E. De Luna. LMs4TNT, Java tool to convert xy coordinates to a TNT data block. jt4tnt v1.0, jan/21/2016. url: http://www.filogenetica.org/Java_tool/lms4tnt.htm (date accessed: xxxxxxx).

Hennig XXXI Workshop: Scripting with TNT, Riverside, CA

Participantes del taller de scripts con TNT

 

Durante las sesiones del taller

Pablo Goloboff y participantes

There has been enough interest expressed for a post-meeting workshop: Scripting in TNT.
The exact location of that, and where you might book accommodations has not been determined yet.
The workshop will run on the 28th, 29th and 30th, June, 2012

Pablo Goloboff (one of the co-authors of the program) and Mark Siddall (who has experience writing scripts) are offering to give a short, 3-day course on scripting for TNT, in connection with the next meeting of the Willi Hennig Society in Riverside, California (June 23-27, 2012).

TNT is a program for phylogenetic analysis under parsimony. Even David Swofford praises it as a good phylogeny program, and it is widely recognized as one of the most powerful programs for phylogenetic analysis. Casual users find it very difficult, because it presents so many options that it is difficult to begin using it. Thus, the program left Matthew Vavrek totally confused, and The Manual caused irreparable damage to the eyes of poor Paulo Nuin (see the Blind Scientist blog).

The powerful scripting language of TNT makes it possible to use the program for an enormous variety of calculations and tests, with a flexibility far beyond any other single program for phylogenetic analysis. See the script for consistency and retention indices as an example of a very simple script, Siddall's script for partition bootstrapping as something easily accomplished with slightly more knowledge and then as well Pol and Escapa's script for iterative PCR or Goloboff's script for testing delayed character correlation as examples of more complex scripts.

This course (see the syllabus below) would be directed to those people who already have some experience with TNT, those who are capable at least of running an entire standard analysis by means of commands (and, ideally, those with some specific problems which need scripts for resolution). The course will start from the simplest ideas and build up from there; no previous scripting or programming knowledge is required (although it doesn't hurt). It will cover the main aspects of the scripting possibilities, with Goloboff and Siddall tutoring exercises directed at solving gradually more complex problems. The last day will be dedicated to people's projects, helping them design (the initial stage, at least) of their own specific projects. People should bring their own laptops (any operating system is OK).

Course syllabus and more information here >>>

Bigger is better: the largest phylogenetic tree reconstructed. | Archetype

Bigger is better: the largest phylogenetic tree reconstructed. | Archetype

Sunday, May 3rd, 2009 | Cladistics, Phylogeny, Uncategorized

GenBank, the standard database for genetic information maintained by National Center for Biotechnology Information, has been accumulating DNA sequences for some three decades now. Since its creation in the late 1980s, it has become the de facto repository for genetic information– genetic data must now be submitted to GenBank for a paper to be accepted for publication. Most sequence data accumulated is the result of the sum of many “local” taxonomic studies, that have targeted a particular group of organism for a relatively small, but well-known collection of genes. It contents now span over hundreds of genes across all of life’s domains. So, what would happen if you were to take all the sequence information contained in GenBank and analyze it phylogenetically all together in a single, one-step study? Well, that is what Pablo A. Goloboff and coworkers just did, the results of which were published in last week’s online early edition of Cladistics, the international journal of the Willi Hennig Society.

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Lea el comentario completo en:

"Archetype, Ant reconstruction one homology at a time"

blog por Roberto Keller

Cladistics: Analisis de una matriz gigante de >73000 UT

Esto si que es difícil de creer: el análisis cladístico de una matriz "super gigante" de 73060 entidades. Así es, no es error de dedo, más de 73 mil unidades terminales! Este análisis portentoso fue efectuado por un equipo basado en Tucumán (Argentina) liderado por Pablo Goloboff. La referencia del artículo, por ahora solo disponible en linea, es:

Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups
Pablo A. Goloboff, Santiago A. Catalano, J. Marcos Mirande, Claudia A. Szumik, J. Salvador Arias, Mari Källersjö and James S. Farris.
Cladistics
http://dx.doi.org/10.1111/j.1096-0031.2009.00255.x

ABSTRACT
Obtaining a well supported schema of phylogenetic relationships among the major groups of living organisms requires considering as much taxonomic diversity as possible, but the computational cost of calculating large phylogenies has so far been a major obstacle. We show here that the parsimony algorithms implemented in TNT can successfully process the largest phylogenetic data set ever analysed, consisting of molecular sequences and morphology for 73 060 eukaryotic taxa. The trees resulting from molecules alone display a high degree of congruence with the major taxonomic groups, with a small proportion of misplaced species; the combined data set retrieves these groups with even higher congruence. This shows that tree-calculation algorithms effectively retrieve phylogenetic history for very large data sets, and at the same time provides strong corroboration for the major eukaryotic lineages long recognized by taxonomists.

Antes de este logro, la idea de matriz "grande" andaba en los 500-1000 unidades terminales (Uts), y los más ambiciosos se esforzaban por ensamblar y analizar matrices de 1500 a 2000 unidades. Obviamente las dificultades para realizar análisis filogenéticos crecen desmesuradamente con cada unidad agregada a la matriz. Los intentos de exploración del enorme espacio de los arboles con estrategias y software convencional (como PAUP) no permitían ni siquiera ver la posibilidad de intentar el análisis de matrices gigantes. Entonces, Goloboff et al (2009) como lo lograron?
Ademas del trabajo tenaz y laborioso que implica compilar una matriz con tantas unidades terminales y caracteres moleculares y morfológicos, la clave del éxito fueron las capacidades analíticas de este grupo de investigadores usando el software TNT.

Bye bye Super-Trees, bienvenidas las SUPER-MATRICES!!!
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Goloboff, P., Catalano, S., Marcos Mirande, J., Szumik, C., Salvador Arias, J., Källersjö, M., & Farris, J. (2009). Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups Cladistics DOI: 10.1111/j.1096-0031.2009.00255.x
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Wiki de ayuda para usar TNT

Se ha anunciado la disponibilidad del wiki TNT como un recurso de ayuda para los usuarios de este programa.

El término WikiWiki es de origen hawaiano que significa: rápido. "Un wiki, o una wiki, es un sitio web cuyas páginas web pueden ser editadas por múltiples voluntarios a través del navegador web. Los usuarios pueden crear, modificar o borrar un mismo texto que comparten." (http://es.wikipedia.org/wiki/Wiki)

Después de un tiempo de estructuración y edición, el WIKI TNT ya esta listo para los usuarios en general. Siga el enlace abajo para mas información sobre como participar editando contenido o contribuyendo a las discusiones.

http://tnt.insectmuseum.org/index.php/Main_Page

Cladística: Métodos cuantitativos de clasificación (Argentina)

Curso: Métodos cuantitativos de clasificación y uso de TNT
13-17 de abril de 2009
Curso teórico-práctico.
Facultad de Ciencias Agrarias
Esperanza, Santa Fe, Argentina

Director del Curso: Dr. Pablo Goloboff, Docentes Colaboradores: Dr. Marcos Miranda, Lic. Santiago Catalano y Lic. Salvador Arias.

Inscripciones: hasta el 31 de marzo de 2009.

Informes e Inscripción
Secretaría de Posgrado -Facultad de Ciencias Agrarias
Tel: 03496-420639 int 161
posgrado@fca.unl.edu.ar

TNT ahora disponible sin costo

A partir del 20 de Noviembre del 2007, el programa TNT (Tree analysis using New Technology) creado por Pablo Goloboff, James Farris y Kevin Nixon esta disponible sin costo alguno gracias a un subsidio de la sociedad Willi Hennig.

Mas información sobre el programa y la manera de obtenerlo puede ser encontrado siguiendo esta liga.

Aqui pueden leer un review >>>