Software

We have developed a large amount of software that we make freely available.

Mostly these are Bioinformatics programs, but we also provide some general utilities and odds and ends.

We also have more software on our github pages.

AndrewCRMartin ACRMGroup

Bioinformatics software

ProFit
Protein least-squares fitting
BiopTools
A set of command-line tools for handling (primarily) protein structure
NW
A pairwise Needleman and Wunsch sequence alignment program
AVP
Calculates protein void volumes and packing quality
QTree
Space filling pictures using the quad-tree algorithm
MINT
A graphical interface to Andrej Sali's Modeller program
Torsions
Calculates backbone torsion angles from a PDB file
SAPTF
'Sequence Analysis Plugin Tool Framework'
Prodoric
A command-line wrapper to the PRODORIC web site
APAT
'Automated Protein Annotation Tool'

Programming libraries

BiopLib
A library of C routines for general programming and handling protein structure
Atomium
A Python library for reading and handling protein protein structure
 

JavaScript

JSAV
JavaScript sequence alignment viewer
buttons.js
Handle buttons on a navigation bar (just click to download)
lastmodified.js
Print 'last modified' text (just click to download)

Utilities

QLite
A batch queueing system for small farms of machines
Cluster
A program to perform hierarchical cluster analysis on a set of arbitrary vectors
CDoc
A program to generate HTML documentation from C source files

Patches to other software

Mirror
A patch for the popular 'mirror' program
Wdiff
A patch for the GNU 'wdiff' program (V0.5) to fix a bug under Linux

GitHub Pages

AndrewCRMartin
Code written (almost) exclusively by Andrew Martin
Group Members
You can also visit GitHub pages of Group Members.
ACRMGroup
Code written by the group

Installation