Post tagged: phylogenetics

Coloring dendroscope files

How to programatically label phylogenies.

The need had arisen for the tips of a large phylogeny to be labelled in a systematic way. Rather than "point and click" within Dendroscope, this script takes a .den/dendro file and colors the tips according to a "color description" file. This is a simple csv file with taxa ...

Error 1 for Mrbayes

What happens when a make fails.

If this happens to you when trying to compile MrBayes:

% make
gcc -DUNIX_VERSION -DUSE_READLINE -O3 -Wall    -c -o mb.o mb.c
gcc -DUNIX_VERSION -DUSE_READLINE -O3 -Wall    -c -o mcmc.o mcmc.c
gcc -DUNIX_VERSION -DUSE_READLINE -O3 -Wall    -c -o bayes.o bayes.c
bayes.c:45:31: readline/readline ...

TreeMaker

An application for the interactive building of taxonomies.

Background

Biodiversity assessment demands objective measures, because ultimately conservation is an issue of economics, prioritizing the use of limited resources for preserving taxa. The most general framework for such metrics are those that assess evolutionary distinctiveness as judged by how much of a phylogeny is conserved. However, their applicability is ...

Mac5

A program for phylogenetic reconstruction using gapped data.

Background

MAC5 is a program which implements MCMC sampling to estimate a phylogenetic tree from a DNA multiple alignment. What differentiates MAC5 from similar programs (e.g. BAMBE, MrBayes) is its use of five-state sequence evolution models as a means to include the gap information when estimating an alignment. Despite ...

MeSA

Macroevolutionary Analysis & Simulation.

Background

Phylogenies are smoking guns. An evolutionary history carrys in its very shape the fingerprints of every process that effected its creation: extinctions, key adaptations, radiations, colonizations, changes in the tempo and mode of macroevolution.

Unfortunately analysing phylogenies is difficult. The calculations of interest to any investigator are sometimes intricate ...