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bioperl-run

BioPerl wrappers

civctp2

git svn import of http://ctp2.darkdust.net/anonsvn/

clans

clans-old

CLANS (Cluster Analysis of Sequences) clusters RNA, DNA and protein sequences for identifying them.

clans-tools

ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

fasttree

A convenient Makefile for compiling various versions of FastTree

jsdeobfuscator

DEPRECATED: Firefox extension that shows you what JavaScript code runs on a web page, even if it is obfuscated and generated on the fly. Simply open JavaScript Deobfuscator from the Web Developer menu and watch the scripts being compiled/executed.

opsins

pasta

PASTA (Practical Alignment using SATe and Transitivity)

phylogenypipeline

A phylogeny pipeline for building single gene phylogenies, such as opsins

pia2

Modified version of the Phylogenetically Informed Annotation tool (Speiser et al., 2014)

pico_galaxy

Galaxy tools and wrappers for sequence analysis

preselector

Preselector.uni-jena.de: optimize your cloning––a resource for identifying restriction enzymes for preselection reactions

preselector.uni-jena.de

proteindatabase

Download and build BLAST databases from the Uniprot SPROT and TRMBL sequence databases

rapidnj

Fast implementation of the Neighbour-Joining method for phylogenetic inference

sate-tools-linux

spaced-dna

The Spaced Words approach to alignment-free sequence comparison