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mafTools
Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.structureHarvester
Structure Harvester is a program for parsing the output of Pritchard's STRUCTURE and for performing the Evanno method.quick_plot
quick_plot is a python program that plots one or two column flat files from the command line.evolverSimControl
jobTree based python wrapper to run the genome simulation tool suite EvolverassemblAnalysis
Analysis scripts to generate Tables and Figures for Assemblathon 1stem
The R function stem() ported to run on the command line for use in pipes!cairo_visualization_wheel
cairo_visualization_wheel is a Python script that uses matplotlib to create visualization wheels as seen in Alberto Cairo's book The Functional Art http://www.thefunctionalart.com/2012/09/download-three-chapters-of-functional.html (see Figure 3.2).n50PlottingTools
Tools to create plots showing N-statistics for genome assembliessummary
summary() from the R project refactored to run on the command line for use in pipes!authorAffiliations
Script to handle superscripted numbers for academic papers that have many authors (>20) and complex affiliationsmwgAlignAnalysis
Multiple Whole Genome Alignment Testing SuiteavgViewer
Ancestral Variation Graph (AVG) viewer in javascriptmafJoin
mafJoin is a tool for combining pairs of MAF files that share a common sequence.fisherWrightCoalPlotter
A script to make Fisher-Wright Coalescent plots using dot from graphvizspia_c
Signaling Pathway Impact Analysis (SPIA) refactored into CevolverInfileGeneration
Scripts and Makefile to generate infile set for the Evolver suite of genome evolution simulation tools.faMask
Utility to mask fasta formated files using a .bed file to define the regions to mask.StatSigMA-w
Given a multiple sequence alignment and a phylogeny relating the aligned sequences, StatSigMAw assesses every site of the alignment and identifies suspiciously aligned regions in the alignment. Xiaoyu Chen and Martin Tompa, "Comparative assessment of methods for aligning multiple genome sequences". Nature Biotechnology, vol. 28, no. 6, June 2010, 567-572. doi:10.1038/nbt.1637Love Open Source and this site? Check out how you can help us