Code and services
Code and services
- Bayesian estimation of gene family phylogenies and
duplication/loss parameters, et.c., with a species tree used as
A novel tool for visualizing gene family evolution
within a species phylogeny. (Previously known as
"DART", a name collision forced a new name.)
Choosing informative markers in DNA sequences.
- 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.
- Estimate pairwise protein distances using a range of
models and methods. Compatible with Phylip and modelestimator.
- Delineate gene/protein families and compute bootstrap
support-values for the predictions.
- 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.
For those who rather use shell tools than web
services, I have brought some of the features from
over in a set of scripts.
You can now easily have
at your fingertips by using RefSense.
Have you ever wanted to monitor the
progress of a big computation? I have wanted
to avoid having a terminal window occupied
by scrolling numbers and what-not. This simple
script gives you a typical graphical progress bar.
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.
- 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