Pinned Repositories
AADavin
aadavin.github.io
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
RelativeDating
Tools to date with transfers
Zombi
Evolution simulator with extinct lineages
AADavin's Repositories
AADavin/Zombi
Evolution simulator with extinct lineages
AADavin/ALEtutorial
A tutorial on Phylogenetic Reconciliations using ALE
AADavin/RelativeDating
Tools to date with transfers
AADavin/AADavin
AADavin/aadavin.github.io
AADavin/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.
AADavin/CoolStuff
A collection of interesting things you can find online
AADavin/DatingTools
AADavin/flying-dog-beers
AADavin/phylo
Helper scripts for making phylogenies
AADavin/ProkkaMC
MC & Transfer analysis of the Prokaryotic tree
AADavin/Pylogeny
Python framework for phylogenetic tree landscapes
AADavin/QMS
Quick Marker Selection for Species Trees
AADavin/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...
AADavin/ZombiPlotting
Some scripts to plot Zombi results