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1 de julio de 2019

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).

31 de mayo de 2019

Curso de Filogenia y Morfometría Geométrica en Barcelona


Ya está abierta la inscripción para la 9ª edición del curso de Transmitting science "Geometric Morphometrics and Phylogeny "

Fechas: Del 9  al 13 de septiembre de 2019

Profesor:  Dr. Chris Klingenberg (University of Manchester, United Kingdom)

Lugar: Capellades, Barcelona (España)

Más información y matrícula:
https://www.transmittingscience.org/courses/geometric-morphometrics/geometric-morphometrics-phylogeny/

Programa del curso:
 
1. Phylogeny, trees and phylogenetic reasoning.
2. Brief review of geometric morphometrics (Procrustes fit, PCA, etc.).
3. Mapping traits onto phylogenies: squared-change parsimony.
4. Practice: making/editing Nexus files, mapping morphometric data onto the tree (Mesquite, MorphoJ).
5. Phylogenetic signal, morphometric traits and estimating phylogeny.
6. Comparative methods: independent contrasts.
7. Application in morphometrics: evolutionary allometry and size correction.
8. Practice: comparative methods (MorphoJ).
9. Application of comparative methods: morphological integration.
10. Multi-level analyses of integration: inferring evolutionary mechanisms.
11. Application of comparative methods: partial least squares (ecomorphology, etc.).
12. Practice: comparative methods (cont.).
13. Morphometrics, phylogenies and qualitative characters.
14. Disparity and diversification.
15. Presentations of group work.

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