Useful links I often forget
- Batch Entrez
- Phyutility A java program to execute many common tasks in phylogenetic analysis at the command line
- Threaded Blockset Aligner (aka TBA, a genome scale multiple local alignment program.)
- An incredibly fast, memory efficient, frequently updated, MPI and PTHREADS parallelized, maximum likelihood phylogenetic inference program.
- The RAxML-HPC website is often hard to google to find, so here's a link to help my memory. It seems like the author (Alexandros Stamatakis) seems to have moved around quite a bit and not updated pointers on the websites from his labs. Here's the latest manual version I could find also.
- SDSC and Vital-IT web based RAxML servers
- Prottest - test models of protein evolution using AIC/BIC/etc. User manual for the console version.
- CiteULike is a great way to organize papers with tags using a bookmarklet system (similar to Connotea, but with a better interface in my opinion)
is a little Java app that will populate most of your entries
with PDFs of the papers and also allow you to download them
locally (neat!) Use the "Download offline version" link and
run syncuthink_standalone Folder/SyncUThink.sh (for Mac/Linux)
or SyncUThink.bat (for PC).
- BEST a modification of MrBayes to jointly estimate gene trees and species trees. Pretty cool! Unfortunately, at least last time I tried, it won't do MPI.
- STAR RNAseq aligner
- LaTeX is a document formatting system based on the typsetting language TeX. I'm just getting started using it to write my dissertation, so here are some helpful links.
- Wikibooks LaTeX book has a lot of info and some very helpful examples
- UT Dissertation and LaTeX Resources Page has a bunch of resources including an explanation of graphics handling and their own style and dissertation writing guide. It is all so well laid out it makes me wish I was writing my dissertation at UT
- natbib reference sheet is a quick-reference for the natbib package that formats your bibtex entries and generally makes life wonderful.
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