Tree andTrees
- softwares for visualisation and manipulations
"Best" softwares by
category
Under construction - april 2008.
Handle annotation
Comparison
of clusters Reconciled
trees Networks
Web servers
Hudge trees
Explore sequences
PipeLines
Able
to handle external annotations
TreeQ-Vista, uses COG informations to annotate the leavesof a tree with colors. Relationnal databases can be used to annotate.
See hudge
trees
The elaborate program TreeWiz can handle huge trees with
up to 50,000 leaves and lets the user explore such trees by collapsing
and expanding nodes interactively. There is an online version, too
(which has not been maintained and currently seems not to be
functional, but the author offers to update it upon demand): In order
to explore one's own trees rather than the given example trees, one
must give read access to one's home directory to the program Java
applet (in general, this would constitute a somewhat liberal security
policy) and create a new directory with a specific name which must hold
the trees.
Dendroscope
Comparison
of clusters or trees
MAST 16448033
K tree score
Reconciled
trees
a
reconciliation describes how a guest tree, G (e.g., a gene tree in the
case of gene evolution), evolves inside a host tree, S (e.g., a species
tree), and allows the prediction and dating of evolutionary events
(e.g., gene duplications or speciations) corresponding to vertices of G
with respect to S. A special case is the most parsimonious
reconciliation, MPR, i.e., the reconciliation that minimizes the number
of evolutionary events. In order to avoid confusion, we will here use
the term general reconciliation to indicate the set of all possible
reconciliationsprimetv
Networks
SplitsTree 18218099
Web servers
A few programs, however, do have a web interface.
Phylodendron
presents the user with several choices of tree
style and appearance as well as different formats for the output image.
Not all combinations of parameter settings seem to be fully
implemented, though. The images are in black and white and have no
branch length labels (only a rule).
PhyloView is a web based visualization
tool which can illustrate
the potential differences between the deduced phylogeny of a protein
sequence
alignment and the taxonomic relationship of the species of the
sequences. The
user uploads a Newick tree and can then decide any taxonomic partition
for the species
and choose a coloring. Thus, the aim of the program is not merely
displaying Newick
trees, and therefore no further control over the tree image is possible.
http://www.trex.uqam.ca/index.php?action=newick&project=trex
Explore
sequences
Nexplorer Phylo-comparison
PipeLines
Bosque
Mega
Panta rhei
Power
TreeFinder 15222900
T-Rex