Clann

Clann: Investigating phylogenetic information through supertree analyses.

View project on GitHub

What is Clann?.

Clann (the Irish word for "family"), is a free software program designed and written by Chris Creevey with James McInerney.

Clann constructs supertrees and allows exploration of the underlying phylogenomic information in gene trees.

Clann implements several well known supertree methods (including the ability to apply bootstrapping to them) can calculate consensus trees and provides methods to manage sets of gene trees, pruning selected taxa, filtering based on a number of criteria, automatically pruning species-specific duplicates and more.

Also implemented is a gene-tree reconciliation approach to try to utilise genetic information from more than just single-copy gene-trees, this can be used as a criterion for estimating species trees. Feed back on these approaches are welcome!

Finally, Clann can also calculate Robinson-Doulds (RF) and SPR distances between sets of trees, create randomised versions of sets of trees and implementes a PTP test for informativeness (the YAPTP test) of a set of trees provided.

Clann has been continually developed since 2003 and suggestions for new features and tools are welcome.

You can see a list of the many papers that have used Clann at Clanns Google Scholar Page

Where has Clann been described?

Creevey C. J. and McInerney, J. O. (2005) Clann: Investigating phylogenetic information through supertree analyses. Bioinformatics 21 (3): 390-2. pdf

Creevey C.J., Fitzpatrick DA, Philip GK, Kinsella RJ, O'connell MJ, Pentony MM, Travers SA, Wilkinson M, McInerney JO. (2004) Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proc R Soc Lond B Biol Sci. 271(1557):2551-8. pdf

Program and manual

Downlods of the latest build are on the right of this page, and the manual can be found here

A short primer on the use of clann:

Creevey, C.J. and McInerney, J.O. (2009) Trees from Trees: Constructing Phylogenetic Supertrees Using CLANN. In: DNA sequence analysis, Ed. David Posada. Humana Press. 537:139-161. pdf

Support or Contact

Having trouble with Clann? Check out our documentation or contact Chris here.

Installing Clann

  
  to install type:
   "./configure"
  followed by:
	 "make
	 
   Clann will then be located in this directory, this can then be copied to a directory on your path (like '~/bin'). 
   The use of "make install" may not work depending on write privileges
  
 

Using Clann

  
   Usage: "clann -lnh [-c commands file] [tree file]"
   
   Where [tree file] is an optional Nexus or Phylip formatted file of phylogenetic trees
   -l turn on logging of screen output to file "clann.log"
   -n turns off interactive mode - requires commands to be provided in a nexus 'clann block' or with '-c'
   -c  specifies a file with commands to be executed (each seperated by ';')
   -h prints help message
  
  
  The following commands are always available:

  execute	- Read in a file of source trees
  help		- Display this message
  quit		- Quit Clann
  set		- Set global parameters such as optimality criterion for carrying reconstructing a supertree
  !		- Run a shell session, while preserving the current Clann session (type 'exit' to return)
  tips		- Show tips and hints for better use of Clann
  log		- Control logging of screen output to a log file
  
  The following commands are only available when there are source trees in memory:

  Supertree reconstruction:
  hs		- Carry out a heuristic search for the best supertree usign the criterion selected
  bootstrap	- Carry out a bootstrap supertree analysis using the criterion selected
  nj		- Construct a neighbour-joining supertree
  alltrees	- Exhaustively search all possible supertrees
  usertrees	- Assess user-defined supertrees (from seperate file), to find the best scoring
  consensus	- Calculate a consensus tree of all trees containing all taxa
  
  Source tree selection and modification:
  showtrees	- Visualise selected source trees in ASCII format (also can save selected trees to file)
  deletetrees	- Specify source trees to delete from memory (based on a variety of criteria)
  deletetaxa	- Specify taxa to delete from all source trees in memory (i.e. prune from the trees while preserving branch lengths)
  randomisetrees- Randomises the source trees in memory, while preserving taxa composition in each tree
  
  Miscellaneous calculations:
  rfdists		- Calculate Robinson-Foulds distances between all source trees
  generatetrees	- Generate random supertrees & assess  against source trees in memory
  yaptp		- "Yet another permutation-tail-probability" test - performs a randomisation test
  
  Experimental Options:
  reconstruct	- Carry out a gene-tree reconciliation (source trees against a species tree)
  prunemonophylies - Prunes clades which consist of multiple sequences from the same species, to a single representative
  sprdists	- Carry out estimation of SPR distances of real data versus ideal and randomised versions of the data
  
  Type a command followed by '?' in interactive mode to get information on the options available i.e.: "exe ?" Full descriptions of the commands are available in the manual