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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.

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.

compbiosummer2015

Research in Computational Biology at Harvey Mudd College, Summer 2015

competititiverooting

comparing various rooting algorithms for phylogenetic language trees

complete-python-3-bootcamp

Course Files for Complete Python 3 Bootcamp Course on Udemy

compphylo_spr17

Material for the Spring 2017 Computational Phylogenetics class

cppcoreguidelines

The C++ Core Guidelines are a set of tried-and-true guidelines, rules, and best practices about coding in C++

data-science-notes

data-structures-textbook

Repository for source code of the Data Structures online textbook (Niema Moshiri and Liz Izhikevich, 2016)

deep-learning-genomics-primer

Contains files for the deep learning in genomics primer.

dgrp-rna-seq

Codes for the DGRP RNA-Seq analyses

dlcpar

Modeling gene duplication, loss, and coalescence (through parsimony)

domaindlrs

Species tree aware simultaneous reconstruction of gene and domain evolution

eqg

Arnold & Felsenstein's Evolutionary Quantitative Genetics course

erable

Python implementation of the ERaBLE method of Binet et al. (2016)

ficus-rad

Genomics workflow for RAD-seq analysis of Ficus

fucking-algorithm

手把手撕LeetCode题目，扒各种算法套路的裤子。English version supported! Crack LeetCode, not only how, but also why.

graphsage-simple

Simple reference implementation of GraphSAGE.

hyde

Hybridization detection using phylogenetic invariants

ipcoal

Simulation package for getting gene tree distributions and loci / SNPs from input tree topologies and migration / Ne scenarios. Wraps around msprime.

jprime

Probabilistic Inference of Molecular Evolution

macrophy_course

Macroevolution & Phylogenetics Course