Bitbucket repositories

bfca
Bayes Factor Cluster Analysis (BFCA) for the objective selection of congruent sets of calibration hypotheses in a Bayesian statistical framework. ( watchers)

genomics_softrepo
Genomics Software Repository installation recipes ( watchers)

ktreedist
Ktreedist is an opensource computer program written in Perl scripting language that calculates the minimum branch length distance (or K tree score) from one phylogenetic tree to another. ( watchers)

transitions_genomic_differentiation_timema
This repository contains a compilation of programs and scripts used for processing and analysing data for: Riesch R, Muschick M, Lindtke D, Villoutreix R, Comeault AA, Farkas TE, Lucek K, Hellen E, SoriaCarrasco V, Dennis SR, de Carvalho CF, Safran RJ, Sandoval CP, Feder J, Gries R, Crespi BJ, Gries G and Nosil P (2017) Transitions between phases of genomic differentiation during stickinsect speciation. Nature Ecology & Evolution, 1, 0082 http://dx.doi.org/10.1038/s415590170082. More detailed information can be found in the folders for each particular analysis in the Dryad repository http://dx.doi.org/10.5061/dryad.nq67q and in the Online Supplementary Materials. ( watchers)
Ktreedist
Version 1.0, June 2007
Copyright © Víctor SoriaCarrasco & Jose Castresana
Ktreedist is an opensource computer program written in Perl scripting language that calculates the minimum branch length distance (or K tree score) from one phylogenetic tree to another. The K tree score provides a measure of the difference in both topology and branch lengths between two trees after scaling one of them to have a global divergence as similar as possible to the other tree. In order to calculate the K score, the program first calculates the scale factor that approximates as much as possible the global divergence of a comparison tree to that of a reference tree; then it scales the comparison tree by this factor ‘K’. Second, the program calculates the branch length distance of Kuhner and Felsenstein between the scaled comparison tree and the reference tree. Our measure is thus the minimum branch length distance you can get from one tree to another after scaling one of them. It can be useful to compare the shape (variation in branch lengths or local molecular clocks) between two phylogenetic trees independently of the global rates. Ktreedist can be used in any operating system with a Perl interpreter.
 SoriaCarrasco, V., Talavera, G., Igea, J., and Castresana, J. (2007). The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees. Bioinformatics 23, 29542956. [Full text] [PDF]
Download Ktreedist: Ktreedist_v1.tar.gz