Webservers for detection of positively selected residues accounting for 3D protein structure

Three webservers so far that estimate ω (=Ka/Ks=dn/ds) taking into account the protein's tertiary structure (PDB ID):

- SELECTON by Tal Pupko's group at Tel Aviv University

- SWAKK by Laura Landweber's group at Princeton University

- Ka/Ks w/ 3D-windowing by David Liberles' group at the University of Wyoming

RAxML black box

RAxML comes now in a new webserver flavor called RAxML Black Box. This is in addition to the RAxML webserver on the CIPRES Portal.

Accepts multiple outgroups (thanx, Alexis :-), does DNA and AA (not combined), accepts partitioned alignment (mixed models), emails a link to the results URL.

Brought to you by Alexandros Stamatakis & Jacques Rougemont.

rename it with a script

Although there are nice little programs for OSX that rename file names and extensions, like Renamer4Mac, NameChanger and FileSorter, it's always good to have something simple handy, like a script.

in AppleScript: Nem

in Perl: here and here (Linux)

my favorite is a loop in Unix to rename file extensions:

1) if you know what your extensions are:

#!/bin/bash

for i in *fasta
do
mv "$i" "`echo $i | sed -e 's/fasta/fas/'`"
done

for i in *fas
do
cat "$i" | sed -e 's/\.fasta\"/\.fas\"/g' > out
mv out "$i"
done

2) if you prefer an interactive script that will ask you what extension names you want to change from/to:

#!/bin/bash

echo -n "enter old: "
read old
echo -n "enter new: "
read new

for i in *.$old
do
mv "$i" "`echo $i | sed -e "s/$old/$new/"`"
done

The shell scripts were kindly written by my friend Ricardo Baratto

Automating Nested Clade Analysis

TCS and GeoDis are the programs to use for NCA, but recently two programs came out that automate NC inference: AUTOINFER and ANeCA.

Addendum (30 Oct 2007)
Panchal & Beaumont (2007) of ANeCA report that Ai-bing Zhang of AUTOINFER has noted that there are some issues in the program that require resolution and that it has temporarily been withdrawn.

Trees: stop fighting!

Tree reconciliation in host-parasite coevolution or in gene-tree fitting has been a long-standing issue in evolutionary biology. Here's some programs that try to bring peace...

TreeMap: for cophylogeny mapping.

TreeFitter: for MP tree-fitting.

SoftParsMap: maps gene trees onto species trees using soft parsimony.

gtp: species tree reconciliation and gene tree parsimony.

UREC: for computing unrooted gene and rooted species tree reconciliation.

CopyCat: easy & fast access to co-phylogenetic analyses. has a wrapper for ParaFit that tests for the association of host and parasite phylogenies.

PriMETV: visualizes tree-within-tree phenomena.

bioinformatics dashboard widgets

Check out ~20 bioinformatics dashboard widgets for OSX Tiger. everything from genetic codes, aminoacid/nucleotide properties, to NCBI BLAST and Entrez. cool!

See the Tree?

Some programs I use to display trees in OSX. Some allow the user to modify trees.

TreeViewX: the industry standard for simple tree visualization.

TreeEdit: views and manipulates trees, re-roots, simulates trees.

FigTree: nice graphical tree viewer.

TreeIllustrator: not only it displays and fiddles with trees, but also has a built-in ToL browser/search engine.

TreeStat: calculates tree statistics (balance, shape, length, popgen).

Phylodendron: draws trees on a webserver or locally (Java app).

TreeJuxtaposer: displays and compares/compresses trees. needs GL4java.

ArboDraw: tree editing with sequence annotation functionality.

TreeMaker: builds taxonomies with species richness data.

TreeSetViz: visualizes tree sets in treespace as a Mesquite module.

Comparing alignments

AliComp [webserver] - compares two DNA or aminoacid alignments.

SOAP [Java cross-platform program] - compares multiple alignments to the user-defined reference alignment in order to identify unstable (i.e. unreliable) characters.