Code and services

The BESST scaffolder

A fast scaffolder with great accuracy, built on a method for unbiased estimation of contig distance.

PrIME

Bayesian estimation of gene family phylogenies and duplication/loss parameters, et.c., with a species tree used as prior information.

Note the wiki with documentation! (And forget about old web pages on SourceForge, Google Code, and our SciLifeLab domain...)

PrIMETV

A tool for visualizing gene family evolution within a species phylogeny. This service is unfortunately still out of service.

Excap

Choosing informative markers in DNA sequences.

modelestimator

Estimate your own amino acid rate matrices and produce output for PAML and FASTA. This program implements a robust method which is described in a JME paper.

Web RefSense.

Formerly known as Biblio, this is an alternative interface to PubMed that supports output in BibTeX and HTML format, automatic web searches, emailing links with citations, and more. Similar alternatives include HubMed, TexMed, BibPubMed, or the BioInfoBank Library.

The code for this web site is available in the repository for RefSense at GitHub.

RefSense

For those who rather use shell tools than web services, I have brought some of the features from Web RefSense over in a set of scripts. You can now easily have PubMed at your fingertips by using RefSense.

avdist

A simple tool for bootstrap analysis of haplotype differences. It computes hamming distance between pairs of sequences sampled from the input sequences and presents average difference and standard devitation of the results after some number of iterations. A previous version of this tool was used for Savolainen et al in Science 2003.

estzmate

Assessing the potential for protein-coding regions in ESTs.

Binary Repeat Align Server.

Align marked (colored) repeats under a repeat-duplication model in the special case of parent-child sequences.