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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.

beagle-lib

general purpose library for evaluating the likelihood of sequence evolution on trees

beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees

beast2

Bayesian Evolutionary Analysis by Sampling Trees

biopython

Official git repository for Biopython (originally converted from CVS)

caffo-coursera

A repository of my Coursera latex code and notes

cytoscape

Cytoscape: an open source platform for network analysis and visualization

datasharing

The Leek group guide to data sharing

datelife

R package containing datelife's core functionality

dendropy

A Python library for phylogenetic scripting, simulation, data processing and manipulation.

eel-pond

mRNAseq assembly, evaluation, and expression analysis

egn2

generax

hmmer

HMMER: biological sequence analysis using profile HMMs

mcl

MCL, the Markov Cluster algorithm, also known as Markov Clustering, is a method and program for clustering weighted or simple networks, a.k.a. graphs.

pargenes

A massively parallel tool for model selection and tree inference on thousands of genes

phylo

Helper scripts for making phylogenies

phylotastic_py

A python library for phylotastic services

python-anti-patterns

An open collection of Python anti-patterns and worst practices.

root_digger

A tool to root phylogenies

rootstrap

seqkit

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

test-repo

tracer

Posterior summarisation in Bayesian phylogenetics

transdecoder

TransDecoder source

treeviewer

Cross-platform software to draw phylogenetic trees

trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly