[Molecular-evolution] Announcing the release of Clann 3.0

Chris Creevey chris.creevey at nuim.ie
Mon Oct 10 16:58:48 EST 2005


We wish to announce the release of Clann version 3.0. This version has 
some significant advances (as described below).
See the website at:   http://bioinf.nuim.ie/software/clann/

For those that don't know Clann.
Clann is a free software tool licenced under GPL for combining 
phylogenetic information. Primarily its focus is on supertrees but it 
also carries out consensus analyses. Clann allows the user to analyse 
their data using 5 different supertree techniques as well as consensus 
approaches. The focus of the software is to allow the user to explore 
their data, so Clann comes equipped with many ways of exploring signal 
within a dataset.
	


Advances in this version:
• The need for the installation of readline for Mac OS X has been 
eliminated.
• 	Fixed Several bugs
	• 	New Criterion added: Average Consensus. Missing Data estimated 
using either an ultrametric or 4 point condition estimate.
	• 	NJ tree can be created using the command 'nj'. This is a 
neighbor-joining tree of an average consensus distance matrix of the 
data.
	• 	Neighbor-joining tree can be used as a starting tree for heuristic 
searches.
	• 	'Showtrees' command added. This allows the user to view selections 
of the sourcetrees as ascii trees on the screen. The user can select 
the trees to be displayed according to their size, taxa compliment, 
score against the best supertree or according to the name of the trees. 
The selection can be saved to file.
	• 	Specific weights can be assigned to individual source trees.
	• 	'Excudetrees' and 'Includetrees' commands added. This allows the 
user to either exclude or include trees from the analysis according to 
the size of the tree, the taxa compliment, the score of the tree 
against a predefined supertree or according to the name given to the 
tree.
	• 	'Deletetaxa' command added. This allows the user to select a taxon 
for deletion from the dataset. This has the effect of pruning the taxa 
from each of the source trees in which it appears. Source trees that 
have fewer than 4 taxa after any taxa are deleted are removed from the 
dataset.
	• 	'Generatetrees' command added. This allows the user to generate 
random supertrees and assess them against the source tree data (or 
against randomised of idealised versions of the source trees). The 
results from the generation of supertrees are displayed as a histogram. 
Statistics about the distribution are also calculated. This command 
also allows the user to create (and save to file) randomised or 
idealised version of their data.
	• 	'Consensus' command added. This allows Clann to carry out a 
consensus analysis of all the universally distributed trees (those 
trees that have all the taxa) in the source tree dataset. The user can 
choose from doing a majority-rule, or strict consensus. The results are 
displayed to screen in a graphical ascii format. This means that clann 
can now be used for the summary of bootstrap proportions from 
phylogenetic analyses.
	• 	Clann now also calculates a consensus tree from any bootstrap 
analyses it carries out.
	• 	Robinson-foulds distances can now be calculated from the 
sourcetrees dataset using the command 'rfdists'. For each comparison 
between two source trees, taxa are pruned from both trees until only 
the taxa that are shared by both trees remain. The results of these 
calculations are saved to file. The user has the choice of matrix or 
vector format.
	• 	Clann now reads nexus format files. The file may contain 
translation tables or not and this also allows the inclusion of a 
'clann block'. This is a set of commands that are to be carried out on 
the data in the file. Clann will ignore any data blocks that are not 
relevant to it.
	• 	When a dataset is executed (loaded into memory) Clann will now also 
display a summary of the distribution of sizes of trees.
	• 	Clann will now "catch" ctrl-c signals so that a search of 
tree-space may be aborted early. Clann will display the best supertree 
found before the ctrl-c signal was sent.









Dr. Christopher J. Creevey
Bioinformatics and Pharmacogenomics Laboratory,
Department of Biology,
National University of Ireland, Maynooth
Co. Kildare
Eire.

e: chris.creevey at may.ie
p: + 353 1 708 6043
f: + 353 1 708 3845
w: http://bioinf.may.ie/
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