Pinned Repositories
advent-of-code-2018
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.
ALE-pipeline
nextflow pipeline to automate analysis using ALE (https://github.com/ssolo/ALE)
Barcoding-Analysis
Biodiversity-pipeline
Pipeline to characterize and analyse fungal microbiomes
haloarchaea-evolution
InteractionPotential
PhyloMagnet
screening metagenomes for arbitrary lineages, using gene-centric assembly methods and phylogenetics
picozoa-scripts
singularity-container
maxemil's Repositories
maxemil/PhyloMagnet
screening metagenomes for arbitrary lineages, using gene-centric assembly methods and phylogenetics
maxemil/ALE-pipeline
nextflow pipeline to automate analysis using ALE (https://github.com/ssolo/ALE)
maxemil/picozoa-scripts
maxemil/InteractionPotential
maxemil/singularity-container
maxemil/advent-of-code-2018
maxemil/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.
maxemil/Barcoding-Analysis
maxemil/Biodiversity-pipeline
Pipeline to characterize and analyse fungal microbiomes
maxemil/haloarchaea-evolution
maxemil/bioconda-recipes
Conda recipes for the bioconda channel.
maxemil/bistorta-vivipara
Scripts and commands for the publication 'Host generalists dominate fungal communities associated with alpine knotweed roots: a study of Sebacinales'
maxemil/cr-testing-example
maxemil/ete
Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
maxemil/FUNGuild
FUNGuild: parsing OTUs into functional guilds
maxemil/git-archaeology
Lesson on archaeology with Git.
maxemil/korarchaeota-scripts
maxemil/maxemil.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
maxemil/megan-ce
MEGAN Community Edition
maxemil/miniasm
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
maxemil/misc-scripts
maxemil/MockCommunity
maxemil/nothofagus-metabarcoding
Scripts associated with the paper 'Ectomycorrhizal fungal communities in andean-patagonian Nothofagus forests'
maxemil/originations-placement
maxemil/PhyloMagnet-benchmarks
Benchmarks for https://github.com/maxemil/PhyloMagnet
maxemil/PhyloMagnet-manuscript
maxemil/picozoa-workflow
maxemil/recPhyloXML
PhyloXML inspired format to represent reconciliations
maxemil/rickettsiales-evolution