vhsvhs

phylobot-django

PhyloBot is a Django web application for composing, running, and viewing PhyloBot jobs.

asr-pipeline

A software pipeline for aligning sequences, inferring ML phylogenies, reconstructing ancestors, and more

anccomp

Identification of functional genetic loci

simgenome

SimGenome is a quantitative model of gene transcription regulatory circuit evolution. SimGenome incorporates three major aspects of this process: (i) DNA-binding thermodynamics, (ii) non-equilibrium gene expression patterns, and (iii) population structure and evolution.

prob_motif

What is the probability of a cis-regulatory motif occurring by chance?

ArayProbeCollapse

Collapse microarray data

ArrayProbeCollapse

Collapse microarray data

bedgraph2wig

Convert BED graph files into wiggle tracks (WIG). This allows genome sequencing data to be viewed as WIG files within MochiView.

chipseqbot

A Web Application that Automates ChIP-Seq Analysis

fogasr

An ancestral analysis of the sequences analyzed previously by Fungal Orthogroups

lazarus

ndt80-chipseq-em

phylowidgets

A collection of Python-based widgets for manipulating sequence alignments, phylogenies, and reconstructed ancestors.

ratflic

Reconstructing ancestors to find functional loci in cancer

SeqTools

Tools for analyzing high-throughput sequencing data

trna_evo

This is analysis pipeline used to make Figure 3 in [Yona, Bloom-Ackerman, et al., eLife 2013], available at this URL: [http://www.ncbi.nlm.nih.gov/pubmed/24363105]. This project analyzes the evolution of tRNAs, from across the tree of life. How prevalent is anticodon switching?