[Molecular-evolution] Release of Clann 3.0

James McInerney james.o.mcinerney at nuim.ie
Tue Oct 11 11:39:10 EST 2005

Firstly, apologies for cross-posting or if this email is
unsolicited/unwanted.  However, we would be grateful if you would please
pass this email on to any colleagues you think might be interested.
Otherwise, delete it immediately, and apologies once again.

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
€  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
 €  Neighbor-joining tree can be used as a starting tree for heuristic
 €  '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
 €  '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
 €  '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.

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