Credential Management Service Client

myproxy

Credential Management Service Client

MyProxy is open source software for managing X.509 Public Key Infrastructure (PKI) security credentials (certificates and private keys). MyProxy combines an online credential repository with an online certificate authority to allow users to securely obtain credentials when and where needed. Users run myproxy-logon to authenticate and obtain credentials, including trusted CA certificates and Certificate Revocation Lists (CRLs).
Running the command line tool WSClean on a MWA observation

wsclean

Fast generic widefield interferometric imager

WSClean (w-stacking clean) is a fast generic widefield imager. It uses the w-stacking algorithm and can make use of the w-snapshot algorithm. As of Feb 2014, it is 2-12 times faster than CASA's w-projection, depending on the array configuration. It supports full-sky imaging and proper beam correction for homogeneous dipole arrays such as the MWA.
Partial Order Alignment for multiple sequence alignment

poa

Partial Order Alignment for multiple sequence alignment

POA is Partial Order Alignment, a fast program for multiple sequence alignment (MSA) in bioinformatics. Its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment. Partial order alignment is an approach to MSA, which can be combined with existing methods such as progressive alignment. POA optimally aligns a pair of MSAs and which therefore can be applied directly to progressive alignment methods such as CLUSTAL. For large alignments, Progressive POA is 10-30 times faster than CLUSTALW.
simulate the evolution of nucleotide or amino acid sequences

seq-gen

simulate the evolution of nucleotide or amino acid sequences

Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution.
random number/character generator

rand

random number/character generator

Script to create an HTML report of MP3 files in a directory

mp3report

Script to create an HTML report of MP3 files in a directory

A customizable program to scan a list of (sub)directories, creating a report from an HTML template. Also calculates various statistics and each song's playing time. Supports ID3 and ID3v2 tags.