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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.

aletutorial

A tutorial on Phylogenetic Reconciliations using ALE

coolstuff

A collection of interesting things you can find online

datingtools

flying-dog-beers

phylo

Helper scripts for making phylogenies

prokkamc

MC & Transfer analysis of the Prokaryotic tree

pylogeny

Python framework for phylogenetic tree landscapes

qms

Quick Marker Selection for Species Trees

relativedating

Tools to date with transfers

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...

zombi

Evolution simulator with extinct lineages

zombiplotting

Some scripts to plot Zombi results