I develop most of my own tools. My preferred programming languages for these are Golang (https://golang.org/) and Python/Cython. You should feel free to use any of them. Documentation can be a bit sparse (although the command line options for Golang executables should get you pretty far), so it would probably be best to get in touch if you are interested in using something.

cophymaru

https://github.com/carolinetomo/cophymaru

Golang package for Bayesian phylogenetic inference and fossil placement using continuous traits.

greedo

https://github.com/carolinetomo/cophycollapse

Parametric unsupervised learning of mosaic evolutionary structure in datasets of quantitative traits.

clusterlen

mandos

https://github.com/carolinetomo/mandos

Python library for phylogenetic analysis of stratigraphic ranges, continuous and discrete morphological traits that specialises in identifying direct ancestors using information criteria.