Adrián A. Davín's repositories
ALEtutorial
A tutorial on Phylogenetic Reconciliations using ALE
RelativeDating
Tools to date with transfers
ALE
Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.
phylo
Helper scripts for making phylogenies
ProkkaMC
MC & Transfer analysis of the Prokaryotic tree
Pylogeny
Python framework for phylogenetic tree landscapes
tailorsdrawer
**Un cajón de sastre** (a tailor's drawer) is a Spanish expression to mean a place or a container where you put all the things that do not fit anywhere else. Having said that, I guess that it must be clear what the content of this repository is...
ZombiPlotting
Some scripts to plot Zombi results