Pinned Repositories
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.
An-Introduction-To-Applied-Bioinformatics
Interactive lessons in bioinformatics.
ASTRAL
Accurate Species TRee ALgorithm
aws-scripts
BactDating
Bayesian inference of ancestral dates on bacterial phylogenetic trees
bds-files
Supplementary files for my book, "Bioinformatics Data Skills"
bpp
Bayesian analysis of genomic sequence data under the multispecies coalescent model
coalhmm
CoalHMM
compbio
Python libraries and utilities for computational biology
compbioftw
Essential introductory materials to get into computational biology.
eeiyowei's Repositories
eeiyowei/Taming-the-BEAST-2019-Sydney-Lectures
Repository for lectures held at the 2019 TTB workshop at the University of Sydney.
eeiyowei/Misc.Statistics.Genetics.Models
A collection of functions for statistics, population genetics, phylogenetics, and other models. Please cite relevant publications and contact Rich Adams before using any of these functions.
eeiyowei/Data-Structures-Textbook
Repository for source code of the Data Structures online textbook (Niema Moshiri and Liz Izhikevich, 2016)
eeiyowei/macrophy_course
Macroevolution & Phylogenetics Course
eeiyowei/bds-files
Supplementary files for my book, "Bioinformatics Data Skills"
eeiyowei/STRIDE
STRIDE: Species Tree Root Inference from Gene Duplication Events
eeiyowei/Nine_Chapter_Senior
Classical and important problems for interview
eeiyowei/DomainDLRS
Species tree aware simultaneous reconstruction of gene and domain evolution
eeiyowei/scripts
Script for transcriptome workshop at Botany 2018
eeiyowei/phyloscripts
Helper scripts for processing and visualization of phylogenetics datasets
eeiyowei/Olave_etal2017-MEE
Detecting Hybridization by Likelihood Calculation of Gene Tree Extra Lineages given Explicit Models
eeiyowei/jprime
Probabilistic Inference of Molecular Evolution
eeiyowei/TreeShrink
Implementation of the TreeShrink problem
eeiyowei/seq2seqModel
Pytorch implimentation of Sequence-to-Sequence Learning with Attentional Neural Networks
eeiyowei/Data-Science-Notes
eeiyowei/parsimony_scorer
Builds and scores evolutionary trees based on newick-format strings and nexus files of data
eeiyowei/PHYLDOG
Software for estimating species tree and gene trees in the presence of duplications and losses
eeiyowei/erable
Python implementation of the ERaBLE method of Binet et al. (2016)
eeiyowei/ficus-rad
Genomics workflow for RAD-seq analysis of Ficus
eeiyowei/CompPhylo_Spr17
Material for the Spring 2017 Computational Phylogenetics class
eeiyowei/dlcpar
Modeling gene duplication, loss, and coalescence (through parsimony)
eeiyowei/phylosim
An R package for the Monte Carlo simulation of sequence evolution
eeiyowei/CompBioSummer2015
Research in Computational Biology at Harvey Mudd College, Summer 2015
eeiyowei/PhyloPostprocessing
Little scripts for handling phylogenetic trees
eeiyowei/compbio
Python libraries and utilities for computational biology
eeiyowei/coalhmm
CoalHMM