Program and Scripts
This OS X Dashboard Widget displays a "cheat sheet" style summary of selection of Emacs commands:
You can download it from here:
One of the great strengths of Git is the multiple and flexible ways of handling remote repositories. Just like Subversion, they can be "served" out of a location, but more generally, if you can reach it from your computer through any number of ways (ssh, etc.), you can git it.
YonderGit wraps up a number of a common operations with remote repositories: creating, initializing, adding to (associating with) the local repository, removing, etc.
You can clone your own copy of the YonderGit code repository using:
This OS X Dashboard Widget displays a "cheat sheet" style summary of selection of Git commands that are commonly used in most development workflows:
You can download it from here:
The following script takes a space separated list of GenBank numbers as input, and then uses BioPython to download the corresponding sequences from GenBank, strips off all non-coding nucleotides, gives the sequences sensible names, and assembles them into a FASTA file.
msBayes is a suite of tools that support a Approximate Bayesian Computation approach for phylogeographic analysis, estimation and hypothesis testing.
msBayes is a suite of tools that support a Approximate Bayesian Computation approach for phylogeographic analysis, estimation and hypothesis testing. The following Python script can be used to ensure that various data files produced by programs in the msBayes pipeline all have the same number and type of columns.
Things to note regarding the operation of the script:
Here is a quick-and-dirty script to convert FASTA files to NEXUS:
Introduction
Syrupy is a Python script that regularly takes snapshots of the memory and CPU load of one or more running processes, so as to dynamically build up a profile of their usage of system resources.
SumTrees is a program by myself and Mark T. Holder to summarize non-parameteric bootstrap or Bayesian posterior probability support for splits or clades on phylogenetic trees.
It is part of the DendroPy Python library for phylogenetic computing, and has its home page at:
bootscore is a program that maps non-parametric bootstrap support for nodes/branches on topology (typically a topology resulting from a best tree search on phylogenetic data).
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