La Folie, Quo Vadis, Evo-Devo?

http://dambe.bio.uottawa.ca/software.asp
DAMBE (Software package for extensive data analysis in molecular biology and evolution, for Windows ME/2000/XP/VISTA and Linux)
 

Many methods of ortholog inference have been proposed, and their comparative performance has been reviewed.
These methods belong to the two major classes of approaches:
1. identify all homologs in a set of species and then attempt to distinguish between orthologs and paralogs by analyzing the distribution of the genes from different species
across the tips of the tree

 
 
 

an integrated system for functional investigation of microRNAs
http://mirgator.kobic.re.kr:8080/MEXWebApp/

Detecting Sequence
Polymorphisms Associated with Meiotic Recombination Hotspots

 
LDsplit is
a novel computational approach for detecting association of recombination
hotspots with genetic polymorphisms.

OGree
Create genome trees of prokaryotes
 
SEMPHY

ProPhylER
http://www.prophyler.org/index.html
ProPhylER provides predictive evolutionary analyses of eukaryotic proteins.
ProPhylER puts comprehensive constraint data on tens of thousands of
eukaryotic proteins, represented by hundreds of thousands of individual
sequences, at the fingertips of the researcher.

http://probcons.stanford.edu/
PROBCONS is an efficient protein multiple sequence alignment
program,

http://www.compbio.dundee.ac.uk/www-pips/
 

BioTapestry (畫network用的)
http://www.biotapestry.org/index.html
BioTapestry is an interactive tool for building, visualizing, and simulating genetic regulatory networks. Here are some
uses of BioTapestry